Enzymatic production of alcohol esters for recovery of diols produced by fermentation

ABSTRACT

Diols produced in fermentation are processed in broth by esterification of the product diol with a carboxylic acid (e.g., fatty acid) and a catalyst (e.g., lipase) capable of esterifying the product diol, such as 1,3-propanediol, with the carboxylic acid to form the diol esters. The diol esters can be extracted from the broth, and the product diol recovered from the diol esters. The carboxylic acid can also serve as an extractant for removal of the diol esters from the fermentation medium.

This application is a divisional of U.S. Ser. No. 13/326,660, filed Dec. 15, 2011, now pending, which is a continuation-in-part of U.S. Ser. No. 13/193,147, filed Jul. 28, 2011 which claims the benefit of U.S. Ser. No. 61/368,429, filed Jul. 28, 2010; U.S. Ser. No. 61/379,546 filed Sep. 2, 2010; U.S. Ser. No. 61/368,444, filed Jul. 28, 2010; U.S. Ser. No. 61/368,436, filed Jul. 28, 2010; U.S. Ser. No. 61/368,451, filed Jul. 28, 2010; and U.S. Ser. No. 13/163,243 filed Jun. 17, 2011 which claims priority to U.S. Ser. No. 61/356,290, filed Jun. 18, 2010, all expired and additionally claims the benefit of U.S. Ser. No. 13/161,168, filed Jun. 15, 2011, now pending which claims the benefit of U.S. Ser. No. 61/356,379, filed Jun. 18, 2010, now expired, and additionally claims the benefit of U.S. Ser. No. 61/440,034, filed Feb. 7, 2011; and U.S. Ser. No. 13/874,737 filed May 1, 2013 which claims the benefit of U.S. Ser. No. 13/163,243 filed Jun. 17, 2011; U.S. Ser. No. 61/356,290, filed Jun. 18, 2010; and U.S. Ser. No. 61/368,429, U.S. Ser. No. 61/368,444, U.S. Ser. No. 61/368,436, U.S. Ser. No. 61/368,451, U.S. Ser. No. 61/379,546, and U.S. Ser. No. 61/440,034 all of the referenced applications incorporated herein by reference in their entirety.

SEQUENCE LISTING

The Sequence Listing associated with this application is filed in electronic form via EFS-Web and hereby incorporated by reference into the specification in its entirety.

FIELD OF THE INVENTION

The present invention relates to the fermentative production of diols, and all related co-products, and processes for recovering diols from fermentation broth employing in situ esterification with a carboxylic acid.

BACKGROUND OF THE INVENTION

Alcohols have a variety of applications in industry and science such as a beverage (i.e., ethanol), fuel, reagents, solvents, and antiseptics. For example, butanol is an alcohol that is an important industrial chemical and drop-in fuel component with a variety of applications including use as a renewable fuel additive, as a feedstock chemical in the plastics industry, and as a food-grade extractant in the food and flavor industry. Accordingly, there is a high demand for alcohols such as butanol, as well as for efficient and environmentally-friendly production methods.

In particular diols, such as 1,2-ethanediol (EDO), 1,3-propanediol (PDO), and 1,4-butanediol (BDO), represent a valuable class of chemicals. Diols are used as monomers in polymerization reactions to synthesize polyesters. The reaction of aforementioned diols with terephthalic acid, for example, yields polyethylene terephthalate (PET), polytrimethylene terephthalate (PTT) and polybutylene terephthalate (PBT), which are highly used chemical products in applications such as beverage and other liquid containers, carpets, engineering resins, and electrical insulators. Accordingly, there is a high demand for diols such as EDO, PDO, and BDO, as well as for efficient and environmentally-friendly production methods.

Production of alcohol utilizing fermentation by microorganisms is one such environmentally-friendly production method. In the fermentative production of PDO and BDO, for example, the final concentrations of these products made by microorganisms in fermentation broths are low. Thus it is a challenge to recover the diols from large volumes of liquid by an economically viable process. Recovery processes typically used including evaporation, distillation, membrane filtration, pervaporation, ion exchange chromotography liquid-liquid extraction, and reactive extraction (Xiu and Zeng (2008) Applied Microbiology and Biotechnology 78:917-926; Clark et al. (2010) WO2010/141780) require large amounts of energy and thus are costly. Extractants with high partition coefficients for diols have not been identified (Malinowski (1999) Biochemical Techniques 13:127-130).

In the production of butanol, in particular, some microorganisms that produce butanol in high yields also have low butanol toxicity thresholds. Removal of butanol from the fermentation vessel as it is being produced is a means to manage these low butanol toxicity thresholds. Thus, there is a continuing need to develop efficient methods and systems for producing butanol in high yields despite low butanol toxicity thresholds of the butanol-producing microorganisms in the fermentation medium.

In situ product removal (ISPR) (also referred to as extractive fermentation) can be used to remove butanol (or other fermentative alcohol) from the fermentation vessel as it is produced, thereby allowing the microorganism to produce butanol (or other fermentative alcohol) at high yields. One ISPR method for removing fermentative alcohol that has been described in the art is liquid-liquid extraction (U.S. Patent Application Publication No. 2009/0305370). In general, with regard to butanol fermentation, the fermentation medium which includes the microorganism is contacted with an organic extractant at a time before the butanol concentration reaches a toxic level. The organic extractant and the fermentation medium form a biphasic mixture. The butanol partitions into the organic extractant phase decreasing the concentration of butanol in the aqueous phase containing the microorganism, thereby limiting the exposure of the microorganism to the inhibitory butanol. In order to be technically and economically viable, liquid-liquid extraction requires contact between the extractant and the fermentation broth for efficient mass transfer of the product alcohol into the extractant; phase separation of the extractant from the fermentation broth (during an/or after fermentation); efficient recovery and recycle of the extractant; and minimal decrease of the partition coefficient of the extractant over a long-term operation.

The extractant can become contaminated over time with each recycle, for example, by the build-up of lipids present in the biomass that is fed to the fermentation vessel as feedstock of hydrolyzable starch. As an example, during the conversion of glucose to butanol, a liquified corn mash loaded to a fermentation vessel at 30 wt % dry corn solids can result in a fermentation broth that contains about 1.2 wt % corn oil generated by simultaneous saccharification and fermentation (with saccharification of the liquified mash occurring during fermentation by the addition of glucoamylase to produce glucose). The dissolution of the corn oil lipids into oleyl alcohol (OA) serving as an extractant during ISPR can result in build-up of lipid concentration with each OA recycle decreasing the partition coefficient for the product alcohol in OA as the lipid concentration in OA increases with each recycle of OA.

In addition, the presence of undissolved solids, from processed biomass feedstocks used for fermentation, during extractive fermentation can negatively affect the efficiency of the alcohol production. For example, the presence of undissolved solids may lower the mass transfer coefficient inside the fermentation vessel, impede phase separation in the fermentation vessel, result in the accumulation of corn oil from the undissolved solids in the extractant leading to reduced extraction efficiency over time, increase the loss of solvent because it becomes trapped in solids and ultimately removed as Dried Distillers' Grains with Solubles (DDGS), slow the disengagement of extractant drops from the fermentation broth, and/or result in a lower fermentation vessel volume efficiency.

Several approaches for reducing the degradation of the partition coefficient of the extractant used in extractive fermentation have included wet milling, fractionation, and removal of solids. Wet milling is an expensive, multi-step process that separates a biomass (e.g., corn) into its key components (germ, pericarp fiber, starch, and gluten) in order to capture value from each co-product separately. This process gives a purified starch stream; however, it is costly and includes the separation of the biomass into its non-starch components which is unnecessary for fermentative alcohol production. Fractionation removes fiber and germ, which contain a majority of the lipids present in ground whole corn resulting in a fractionated corn that has a higher starch (endosperm) content. Dry fractionation does not separate the germ from fiber and therefore, it is less expensive than wet milling. However, fractionation does not remove the entirety of the fiber or germ, and does not result in total elimination of solids. Furthermore, there is some loss of starch in fractionation. Wet milling of corn is more expensive than dry fractionation, but dry fractionation is more expensive than dry grinding of unfractionated corn. Removal of solids including germ containing lipids, from liquefied mash prior to use in fermentation can substantially eliminate undissolved solids as described, for example, in co-pending, commonly owned U.S. application Ser. No. 12/163,243, filed Jun. 17, 2011. However, it would be advantageous if the degradation of the partition coefficient of the extractant caused by contamination by lipid can be reduced even without fractionation or removal of substantially all undissolved solids. Converting the lipids present in a liquefied mash into an extractant that can be used in product removal, including ISPR, is another method of decreasing the amount of lipids that are fed to the fermentation vessel as described, for example, in co-pending, commonly owned U.S. application Ser. No. 13/162,828 and U.S. application Ser. No. 13/162,643, both filed on Jun. 17, 2011.

There is a continuing need for alternative extractive fermentation methods which do not necessitate the partitioning of the product alcohol between the fermentation medium and the ISPR extractant as a means to reduce the toxic effect of the product alcohol such as butanol on the microorganism, and which can also reduce the degradation of the partition coefficient of a fermentation product extractant.

In addition, there is a continuing need for alternative methods for recovering and purifying diols produced by fermentation, which are efficient and less costly than those typically practiced.

SUMMARY OF THE INVENTION

Conversion of a diol produced from a microorganism in a fermentation medium into a diol ester (including diol monoester and/or diol diester) can allow simplified recovery and purification of the diol product. Diol esters can be formed by contacting the diol in a fermentation medium or fermentation product broth with a carboxylic acid (e.g., fatty acids) and a catalyst capable of esterifying the diol with the carboxylic acid. Moreover, the carboxylic acid can serve as an ISPR extractant or a post-fermentation extractant, or a component of an extractant, into which the diol esters partition. Accordingly, the invention provides a method for recovering a diol from a fermentation process comprising:

-   -   a) providing a fermentation medium or fermentation product broth         containing a diol;     -   b) contacting the diol in the fermentation medium or         fermentation product broth with at least one carboxylic acid and         at least one catalyst capable of esterifying the carboxylic acid         with the diol to form diol esters of the carboxylic acid in the         presence of an organic solvent which is present at a         concentration sufficient to produce a two-phase mixture;     -   c) separating the diol ester-containing organic phase from the         aqueous phase; and     -   d) hydrolyzing the diol ester into carboxylic acid and diol; and     -   e) recovering the diol.         In another embodiment the invention provides a method for         producing a diol from a biomass feedstock comprising:     -   (a) providing a biomass feedstock;     -   (b) liquefying the biomass feedstock to create a feedstock         slurry comprising oligosaccharides;     -   (c) saccharifying the oligosaccharides of the feedstock slurry         to produce fermentable sugars;     -   (d) fermenting the fermentable sugars using a microorganism to         produce a diol in a fermentation medium or a fermentation         product broth;     -   (e) contacting the diol in the fermentation medium or         fermentation product broth with at least one carboxylic acid and         at least one catalyst capable of esterifying the carboxylic acid         with the diol to form diol esters of the carboxylic acid in the         presence of an organic solvent which is present at a         concentration sufficient to produce a two-phase mixture;     -   f) separating the diol ester-containing organic phase from the         aqueous phase;     -   g) hydrolyzing the diol ester into carboxylic acid and diol; and     -   h) recovering the diol.         wherein optionally steps (c) and (d) occur concurrently,         optionally steps (d) and (e) occur concurrently, or optionally         steps (c), (d), and (e) occur concurrently. In another         embodiment the invention provides a fermentation broth         composition comprising:     -   (a) a microorganism capable of producing a product diol;     -   (b) fermentable sugars;     -   (c) a product diol;     -   (d) at least one carboxylic acid;     -   (e) a catalyst capable of extracellularly esterifying a         carboxylic acid with said product diol into carboxylic acid diol         esters; and     -   (f) carboxylic acid diol esters.         In yet another embodiment the invention provides a fermentation         product broth composition comprising:     -   a) a product diol;     -   b) at least one carboxylic acid;     -   c) a catalyst capable of extracellularly esterifying a         carboxylic acid with said product diol into carboxylic acid diol         esters; and     -   d) carboxylic acid diol esters.

In the present methods the carboxylic acid can be supplied to the fermentation vessel or a post-fermentation vessel containing the fermentation product broth. When a biomass feedstock is used, the carboxylic acid can be derived from biomass supplying fermentable carbon feed to the fermentation vessel. Lipids present in the biomass feedstock can be catalytically hydrolyzed to carboxylic acid and the same catalyst (e.g., enzymes) can esterify the carboxylic acid with the alcohol (e.g., diol); lipids can also be directly transesterified by the catalyst to produce diol esters. The catalyst can be supplied to the feedstock prior to fermentation, supplied to the fermentation vessel before or contemporaneously with the supplying of the feedstock, or supplied to the fermentation vessel or to a post-fermentation vessel containing fermentation product broth. When the catalyst is supplied to the fermentation vessel or post-fermentation vessel, alcohol esters can be obtained by hydrolysis of the lipids into carboxylic acid and concurrent esterification of carboxylic acid with a diol present in the fermentation vessel or post-fermentation vessel; lipids can also be directly transesterified with a diol by the catalyst to produce alcohol esters. Carboxylic acid and/or native oil not derived from the feedstock can also be fed to the fermentation vessel or post-fermentation vessel, with the native oil being hydrolyzed into carboxylic acid. Carboxylic acid and/or native oil not derived from the feedstock can be fed into the fermentation vessel or post-fermentation vessel in an amount sufficient such that a two-phase mixture comprising an organic phase and an aqueous phase is formed. As such, in some embodiments, any carboxylic acid not esterified with the diol can serve as the extractant or as a part thereof. The extractant containing diol esters can be separated from the fermentation medium or fermentation product broth, and the dool can be recovered from the extractant. The extractant can be recycled to the fermentation vessel or post-fermentation vessel. In addition, unfractionated grain can be used as feedstock without separation of lipids therein, since the lipids can be catalytically hydrolyzed to carboxylic acid, thereby decreasing the rate of build-up of lipids in the extractant.

In various embodiments, the production of a diol and the production of diol esters occur simultaneously or sequentially. In one embodiment, a feedstock in the fermentation process comprises one or more fermentable sugars. In another embodiment, the feedstock in the fermentation process comprises one or more fermentable sugars derived from corn grain, wheat, rye, barley, sugar cane, sugar beets, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat straw, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum plant material, soybean plant material, components obtained from milling of grains, cellulosic material, lignocellulosic material, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof. In one embodiment, the method further comprises providing a native oil and converting at least a portion of the native oil into carboxylic acid by contacting the oil with one or more enzymes. In one embodiment, the carboxylic acid comprises fatty acids. In another embodiment, the carboxylic acid comprises 12 to 22 carbons. In one embodiment, the carboxylic acid is a mixture of carboxylic acids. In another embodiment, the diol esters of the carboxylic acid are diol esters of fatty acids. In one embodiment, the catalyst is an enzyme capable of esterifying the carboxylic acid with the diol to form diol esters of the carboxylic acid. In another embodiment, the enzyme is an esterase, lipase, phospholipase, or lysophospholipase.

In one embodiment, the method further comprises separating an oil stream from a feedstock slurry. In one embodiment, the method further comprises obtaining an oil from the oil stream and converting at least a portion of the oil into carboxylic acid. In one embodiment, the feedstock slurry is separated by decanter bowl centrifugation, tricanter centrifugation, disk stack centrifugation, filtering centrifugation, decanter centrifugation, filtration, vacuum filtration, beltfilter, pressure filtration, screen filtration, screen separation, grating, porous grating, flotation, hydroclone, filter press, screwpress, gravity settler, vortex separator, or combination thereof. In another embodiment, the carboxylic acid comprises fatty acids. In one embodiment, the carboxylic acid comprises 12 to 22 carbons. In one embodiment, the method further comprises adding the oil to the fermentation vessel or post-fermentation vessel prior to the step of converting at least a portion of the oil into carboxylic acid. In one embodiment, the method further comprises adding additional carboxylic acid to the fermentation vessel or post-fermentation vessel. In one embodiment, the oil is converted to carboxylic acid after the step of adding the additional carboxylic acid. In another embodiment, the carboxylic acid is corn oil fatty acid, soya oil fatty acid, or a mixture of corn oil fatty acid and soya oil fatty acid. In one embodiment, the oil obtained from the oil stream comprises glycerides and the one or more catalysts hydrolyze the glycerides into fatty acids and glycerol. In another embodiment, the diol esters of carboxylic acid are diol esters of fatty acids. In one embodiment, the catalyst is an enzyme capable of esterifying the carboxylic acid with the diol to form diol esters of the carboxylic acid. In one embodiment, the enzyme is an esterase, lipase, phospholipase, or lysophospholipase. In one embodiment, the method further comprises the step of washing the solids with a solvent. In one embodiment, the solvent is selected from hexane, isobutanol, isohexane, ethanol, petroleum distillates such as petroleum ether, or mixtures thereof. In another embodiment, the solids are processed to form an animal feed product. In one embodiment, the animal feed product comprises one or more of crude protein, crude fat, triglycerides, fatty acid, fatty acid isobutyl ester, lysine, neutral detergent fiber (NDF), and acid detergent fiber (ADF). In another embodiment, the animal feed product further comprises one or more vitamins, minerals, flavoring, or coloring. In one embodiment, the animal feed product comprises 20-35 wt % crude protein, 1-20 wt % crude fat, 0-5 wt % triglycerides, 4-10 wt % fatty acids, and 2-6 wt % fatty acid isobutyl esters. In one embodiment, the step of separating the solids from the feedstock slurry increases the efficiency of the diol production by increasing a liquid-liquid mass transfer coefficient of the diol from the fermentation broth or fermentation product broth to the extractant; increases the efficiency of the diol production by increasing an extraction efficiency of the diol with an extractant; increases the efficiency of the diol production by increasing a rate of phase separation between the fermentation broth or fermentation product broth and an extractant; increases the efficiency of the diol production by increasing recovery and recycling of an extractant; or increases the efficiency of the diol production by decreasing a flow rate of an extractant.

In some embodiments, the step of separating the solids from the feedstock slurry increases the efficiency of the diol production by increasing a liquid-liquid mass transfer coefficient of the diol from the fermentation broth or fermentation product broth to the extractant; increases the efficiency of the diol production by increasing an extraction efficiency of the diol with an extractant; increases the efficiency of the diol production by increasing a rate of phase separation between the fermentation broth or fermentation product broth and an extractant; increases the efficiency of the diol production by increasing recovery and recycling of an extractant; or increases the efficiency of the diol production by decreasing a flow rate of an extractant. In some embodiments the diol is 1,2-ethanediol, 1,2-propanediol, 1,3-propanediol (PDO), 1,4-butanediol (BDO), or 2,3-butanediol.

In some embodiments, recovering diol from the diol esters comprises hydrolyzing the esters into carboxylic acid and diol. In some embodiments, the diol esters are hydrolyzed in the presence of a hydrolysis catalyst. In some embodiments, the diol esters are hydrolyzed in the presence of water and the hydrolysis catalyst comprises an acid catalyst, an organic acid, an inorganic acid, a water soluble acid, or water insoluble acid. In some embodiments, the hydrolysis catalyst comprises an enzyme capable of hydrolyzing the diol esters to form a carboxylic acid and diol. In some embodiments, the enzyme is an esterase, lipase, phospholipase, or lysophospholipase. In some embodiments, enzyme reaction conditions favor enzymatic hydrolysis over esterification. In some embodiments, the enzyme reaction conditions comprise a cosolvent. In some embodiments, fatty acid diol esters, fatty acids, diol, and water are soluble in the cosolvent, and free fatty acids do not react with the cosolvent. In some embodiments, the cosolvent is selected from acetone, tert-butanol, 2-Me-2-butanol, 2-Me-2-pentanol, and 3-Me-3-pentanol. In some embodiments, the enzyme reaction conditions comprise end-product removal. In some embodiments, the end-product is diol or fatty acids. In some embodiments, diol is removed by vacuum distillation, pervaporartion, permselective filtration, gas sparging, or membrane separation. In some embodiments, the fatty acids are removed by precipitation, permselective filtration, or electrophorectically. In some embodiments, the hydrolysis reaction occurs in a reaction vessel. In some embodiments, recovering diol from the diol esters comprises transesterifying the diol esters into diol and fatty acid alkyl esters or acyl glycerides. In some embodiments, the fatty acid alkyl esters comprise fatty acid methyl esters, fatty acid ethyl esters, or fatty acid propyl esters. In some embodiments, the method further comprises providing a native oil and converting at least a portion of the native oil into carboxylic acid by contacting the oil with one or more enzymes. In some embodiments, the enzyme is an enzyme capable of hydrolyzing or transesterifying the diol esters to form diol. In some embodiments, the enzyme is an esterase, lipase, phospholipase, or lysophospholipase. In some embodiments, the carboxylic acid comprises fatty acids. In some embodiments, the carboxylic acid has carbon chain lengths ranging from 12 to 22 carbons. In some embodiments, at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of diol is recovered from the diol esters. In some embodiments, carboxylic acid is recovered from the diol esters. In some embodiments, the method further comprises the steps of removing diol from the fermentation vessel or post-fermentation vessel as extractant stream; and adding the extractant stream to two or more distillation columns. In some embodiments, the distillation column is a super-atmospheric distillation column with a steam heated reboiler. In some embodiments, the method further comprises the steps of recovering water and solvent from the distillation columns; and recycling the water and solvent. In some embodiments, the method further comprises the steps of recovering heat from the distillation process; and recycling the heat to evaporate water. In some embodiments the diol is 1,2-ethanediol, 1,2-propanediol, 1,3-propanediol (PDO), 1,4-butanediol (BDO), or 2,3-butanediol.

The present invention is directed to a fermentation broth comprising (a) a microorganism capable of producing a diol; (b) a fermentable carbon substrate; (c) a product diol; (d) at least one carboxylic acid; (e) a catalyst capable of extracellularly esterifying a carboxylic acid with said diol into fatty acid diol esters; and (f) fatty acid diol esters. In some embodiments the fatty acid diol esters are produced during or subsequent to the fermentation. In some embodiments, the fermentation broth further comprises one or more of the following: acyl glycerides, fatty acids, diol, or oleic acid. In some embodiments, the fermentation broth further comprises a catalyst wherein said catalyst esterifies fatty acids with diol into fatty acid diol esters and hydrolyzes triglycerides into free fatty acids. In some embodiments, the catalyst is one or more lipase enzymes. In some embodiments, the fermentation broth further comprises a saccharification enzyme capable of converting oligosaccharides into fermentable sugar. In some embodiments, the saccharification enzyme comprises glucoamylase. In some embodiments, the fermentable sugar comprises monomeric glucose. In some embodiments, the recombinant microorganism is capable of producing a diol. In some embodiments the diol is 1,2-ethanediol, 1,2-propanediol, 1,3-propanediol (PDO), 1,4-butanediol (BDO), or 2,3-butanediol. The present invention is directed to a fermentation composition comprising (a) a catalyst capable of esterifying free fatty acids with a diol into fatty acid diol esters and optionally capable of hydrolyzing glycerides into free fatty acids; (c) diol; (d) free fatty acids; and (e) fatty acid diol esters formed in situ from esterification of the free fatty acids with the diol using the catalyst. In some embodiments, the composition further comprises oil, wherein the oil comprises glycerides. In some embodiments, the oil, the free fatty acids, and the fermentable carbon substrate are derived from a biomass. In some embodiments, the oil and the fermentable carbon substrate are derived from the same biomass source or from different biomass sources. In some embodiments, the biomass source of the oil is soya or corn oil, and the biomass source of the fermentable carbon substrate is corn. In some embodiments, the free fatty acids are corn oil fatty acids. In some embodiments, the free fatty acids are formed from hydrolysis of at least a portion of the glycerides in the oil using the catalyst. In some embodiments, the composition further comprises at least one of diglycerides and monoglycerides formed from the partial hydrolysis of a portion of the glycerides in the oil using the catalyst. In some embodiments, the composition further comprises glycerol. In some embodiments, the composition further comprises undissolved solids derived from the biomass source of the fermentable carbon substrate. In some embodiments, the composition contains less than about 25 wt % of the undissolved solids. In some embodiments, the composition further comprises a saccharification enzyme capable of converting starch into fermentable sugar. In some embodiments the diol is 1,2-ethanediol, 1,2-propanediol, 1,3-propanediol (PDO), 1,4-butanediol (BDO), or 2,3-butanediol.

In yet another embodiment the invention provides a fermentation product broth composition comprising: (a) a product diol; (b) at least one carboxylic acid; (c) a catalyst capable of extracellularly esterifying a carboxylic acid with said product diol into carboxylic acid diol esters; and (d) carboxylic acid diol esters.

BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES

The accompanying drawings, which are incorporated herein and form a part of the specification, illustrate the present invention and, together with the description, further serve to explain the principles of the invention and to enable a person skilled in the pertinent art to make and use the invention.

FIG. 1 schematically illustrates an exemplary method and system of the present invention, in which a catalyst for alcohol esterification is supplied to a fermentation vessel along with carboxylic acid and/or native oil.

FIG. 2 schematically illustrates an exemplary method and system of the present invention, in which native oil is converted into carboxylic acid using a catalyst, and the carboxylic acid and the catalyst are supplied to a fermentation vessel.

FIG. 3 schematically illustrates an exemplary method and system of the present invention, in which a liquefied biomass is contacted with a catalyst for lipid hydrolysis before fermentation.

FIG. 4 schematically illustrates an exemplary method and system of the present invention, in which a liquefied and saccharified biomass is contacted with a catalyst for lipid hydrolysis before fermentation.

FIG. 5 schematically illustrates an exemplary method and system of the present invention, in which an amount of lipids and undissolved solids are removed from a liquefied biomass before fermentation, and in which the removed lipids are converted into carboxylic acid using a catalyst, and the carboxylic acid and the catalyst are supplied to the fermentation vessel.

FIG. 6 shows the aqueous and solvent phase concentrations of isobutanol produced by fermentation with sucrose as a carbon source. Aqueous phase titer (Panel A) is reported in g/L and the solvent phase species (isobutanol, Panel B and isobutanol as FABE, Panel C. Panel D is the total isobutanol in the solvent phase) in weight percent.

FIG. 7 shows the effective titer of isobutanol, g/L, over time. Effective titer in this example was calculated as described in the text, based on the initial volume of aqueous fermentor broth after inoculation.

FIG. 8 shows the consumption of sugars, reported in glucose equivalents, over time.

DETAILED DESCRIPTION OF THE INVENTION

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present application including the definitions will control. Also, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. All publications, patents, and other references mentioned herein are incorporated by reference in their entireties for all purposes.

Unless otherwise specified, when the following abbreviations are used herein, they have the following meaning:

ADH alcohol dehydrogenase ALS acetolactate synthase AQ aqueous fraction BuO-COFA butyl ester(s) of corn oil fatty acid(s) CALB Candida antarctica lipase B COFA corn oil fatty acid(s) DDGS Dried Distillers' Grains with Solubles DG diglyceride(s) DHAD dihydroxyacid dehydratase

EOR end of run

EtOH ethanol EtO-COFA ethyl ester(s) of corn oil fatty acid(s) FABE fatty acid butyl ester(s) FAEE fatty acid ethyl ester(s) FAME fatty acid methyl ester(s) FFA free fatty acid(s) FOA fluoro-orotic acid HADH horse liver alcohol dehydrogenase IBA isobutanol i-BuOH isobutanol i-BuO-COFA isobutyl ester(s) of corn oil fatty acid(s) i-BuO-oleate iso-butyl oleate i-PrOH isopropanol i-PrO-COFA isopropyl ester(s) of corn oil fatty acid(s) ISPR in situ product removal KARI ketol-acid reductoisomerase KivD ketoisovalerate decarboxylase MAG monoacylglyceride(s) MeBOH 2-methyl-1-butanol MeBO-COFA2-methyl-1-butyl ester(s) of corn oil fatty acid(s) MeOH methanol MeO-COFA methyl ester(s) of corn oil fatty acid(s) MG monoglyceride(s) n-BuOH n-butanol OA oleyl alcohol ORG organic fraction PenOH 1-pentanol PenO-COFA 1-pentyl ester(s) of corn oil fatty acid(s) PrOH 1-propanol PrO-COFA 1-propyl ester(s) of corn oil fatty acid(s) SOFA soya oil fatty acids SSF simultaneous saccharification and fermentation t-BuOH tert-butyl alcohol TG triglyceride(s) 3M3P 3-Me-3-pentanol

In order to further define this invention, the following terms and definitions are herein provided.

As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains,” or “containing,” or any other variation thereof, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers. For example, a composition, a mixture, a process, a method, an article, or an apparatus that comprises a list of elements is not necessarily limited to only those elements but can include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).

Also, the indefinite articles “a” and “an” preceding an element or component of the invention are intended to be nonrestrictive regarding the number of instances, that is, occurrences of the element or component. Therefore “a” or “an” should be read to include one or at least one, and the singular word form of the element or component also includes the plural unless the number is obviously meant to be singular.

The term “invention” or “present invention” as used herein is a non-limiting term and is not intended to refer to any single embodiment of the particular invention but encompasses all possible embodiments as described in the application.

As used herein, the term “about” modifying the quantity of an ingredient or reactant of the invention employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or to carry out the methods; and the like. The term “about” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about,” the claims include equivalents to the quantities. In one embodiment, the term “about” means within 10% of the reported numerical value, alternatively within 5% of the reported numerical value.

“Biomass” as used herein refers to a natural product containing hydrolyzable polysaccharides that provide fermentable sugars including any sugars and starch derived from natural resources such as corn, cane, wheat, cellulosic or lignocellulosic material and materials comprising cellulose, hemicellulose, lignin, starch, oligosaccharides, disaccharides and/or monosaccharides, and mixtures thereof. Biomass may also comprise additional components such as protein and/or lipids. Biomass may be derived from a single source or biomass can comprise a mixture derived from more than one source. For example, biomass may comprise a mixture of corn cobs and corn stover, or a mixture of grass and leaves. Biomass includes, but is not limited to, bioenergy crops, agricultural residues, municipal solid waste, industrial solid waste, sludge from paper manufacture, yard waste, waste sugars, wood and forestry waste. Examples of biomass include, but are not limited to, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, rye, wheat straw, barley, barley straw, hay, rice straw, switchgrass, waste paper, sugar cane bagasse, sorghum, sugar cane, soy, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, flowers, animal manure, and mixtures thereof. For example, mash, juice, molasses, or hydrolysate may be formed from biomass by any processing known in the art for processing the biomass for purposes of fermentation such as by milling, treating, and/or liquefying and comprises fermentable sugar and may comprise water. For example, cellulosic and/or lignocellulosic biomass may be processed to obtain a hydrolysate containing fermentable sugars by any method known to one skilled in the art. Particularly useful is a low ammonia pretreatment as disclosed U.S. Patent Application Publication No. 2007/0031918A1, which is herein incorporated by reference. Enzymatic saccharification of cellulosic and/or lignocellulosic biomass typically makes use of an enzyme consortium for breaking down cellulose and hemicellulose to produce a hydrolysate containing sugars including glucose, xylose, and arabinose. (Saccharification enzymes suitable for cellulosic and/or lignocellulosic biomass are reviewed in Lynd, et al. (Microbiol. Mol. Biol. Rev. 66:506-577, 2002).

Mash, juice, molasses, or hydrolysate may include feedstock 12 and feedstock slurry 16 as described herein. An aqueous feedstream may be derived or formed from biomass by any processing known in the art for processing the biomass for purposes of fermentation such as by milling, treating, and/or liquefying and comprises fermentable carbon substrate (e.g., sugar) and may comprise water. An aqueous feedstream may include feedstock 12 and feedstock slurry 16 as described herein.

“Biomass yield” as used herein refers to the grams of biomass produced (i.e., cell biomass production) per gram of carbon substrate produced.

“Feedstock” as used herein means a feed in a fermentation process, the feed containing a fermentable carbon source with or without undissolved solids, and where applicable, the feed containing the fermentable carbon source before or after the fermentable carbon source has been liberated from starch or obtained from the break down of complex sugars by further processing such as by liquefaction, saccharification, or other process. Feedstock includes or is derived from a biomass. Suitable feedstocks include, but are not limited to, rye, wheat, corn, corn mash, cane, cane mash, barley, cellulosic material, lignocellulosic material, or mixtures thereof. Where reference is made to “feedstock oil,” it will be appreciated that the term encompasses the oil produced from a given feedstock.

“Fermentation medium” as used herein means the mixture of water, sugars, dissolved solids, optionally microorganisms producing alcohol, product alcohol, and all other constituents of the material held in the fermentation vessel in which product alcohol is being made by the reaction of sugars to alcohol, water, and carbon dioxide (CO₂) by the microorganisms present. At the end of a fermentation run the sugars may be depleted from the fermentation medium. From time to time, as used herein the term “fermentation broth” and “fermented mixture” can be used synonymously with “fermentation medium.”

“Fermentation product broth” as used herein means spent fermentation medium containing a product alcohol produced by a microorganism. A fermentation product broth may have been processed to remove any components such as microorganisms.

“Fermentable carbon source” or “fermentable carbon substrate” as used herein means a carbon source capable of being metabolized by the microorganisms disclosed herein for the production of fermentative alcohol. Suitable fermentable carbon sources include, but are not limited to, monosaccharides such as glucose or fructose; disaccharides such as lactose or sucrose; oligosaccharides; polysaccharides such as starch or cellulose; C5 sugars such as xylose and arabinose; one carbon substrates including methane; and mixtures thereof.

“Fermentable sugar” as used herein refers to one or more sugars capable of being metabolized by the microorganisms disclosed herein for the production of fermentative alcohol.

“Fermentation vessel” as used herein means the vessel in which the fermentation reaction is carried out whereby product alcohol such as butanol is made from sugars.

“Liquefaction vessel” as used herein means the vessel in which liquefaction is carried out. Liquefaction is the process in which oligosaccharides are liberated from the feedstock. In some embodiments where the feedstock is corn, oligosaccharides are liberated from the corn starch content during liquefaction.

“Saccharification vessel” as used herein means the vessel in which saccharification (i.e., the break down of oligosaccharides into monosaccharides) is carried out. Where fermentation and saccharification occur simultaneously, the saccharification vessel and the fermentation vessel may be one in the same vessel.

“Sugar” as used herein refers to oligosaccharides, disaccharides, monosaccharides, and/or mixtures thereof. The term “saccharide” also includes carbohydrates including starches, dextrans, glycogens, cellulose, pentosans, as well as sugars.

As used herein, “saccharification enzyme” means one or more enzymes that are capable of hydrolyzing polysaccharides and/or oligosaccharides, for example, alpha-1,4-glucosidic bonds of glycogen, or starch. Saccharification enzymes may include enzymes capable of hydrolyzing cellulosic or lignocellulosic materials as well.

“Undissolved solids” as used herein means non-fermentable portions of feedstock, for example, germ, fiber, and gluten. For example, the non-fermentable portions of feedstock include the portion of feedstock that remains as solids and can absorb liquid from the fermentation broth.

Dried Distillers' Grains with Solubles (DDGS) as used herein refers to a co-product or by-product from a fermentation of a feedstock or biomass (e.g., fermentation of grain or grain mixture that produces a product alcohol). In some embodiments, DDGS may also refer to an animal feed product produced from a process of making a product alcohol (e.g., butanol, isobutanol, etc.).

“Product alcohol” as used herein refers to any alcohol that can be produced by a microorganism in a fermentation process that utilizes biomass as a source of fermentable carbon substrate. Product alcohols include, but are not limited to, C₁ to C₈ alkyl alcohols. In some embodiments, the product alcohols are C₂ to C₈ alkyl alcohols. In other embodiments, the product alcohols are C₂ to C₅ alkyl alcohols. It will be appreciated that C₁ to C₈ alkyl alcohols include, but are not limited to, methanol, ethanol, propanol, butanol, and pentanol. Likewise C₂ to C₈ alkyl alcohols include, but are not limited to, ethanol, propanol, butanol, and pentanol. In addition, product alcohols include diols such as diethylene glycol, 1,2-ethanediol (EDO), 1,2-propanediol, 1,3-propanediol (PDO), 1,4-butanediol (BDO), and 2,3-butanediol. “Alcohol” is also used herein with reference to a product alcohol.

“Diol ester” as used herein refers to any ester that can be produced from a diol and a carboxylic acid, including a diol monoester. a diol diester, and a mixture of diol monoester and diol diester.

“Butanol” as used herein refers with specificity to the butanol isomers 1-butanol (1-BuOH), 2-butanol (2-BuOH), tert-butanol (t-BuOH), and/or isobutanol (iBuOH or i-BuOH or I-BUOH, also known as 2-methyl-1-propanol), either individually or as mixtures thereof. From time to time, when referring to esters of butanol, the terms “butyl esters” and “butanol esters” may be used interchangeably.

“Propanol” as used herein refers to the propanol isomers isopropanol or 1-propanol.

“Pentanol” as used herein refers to the pentanol isomers 1-pentanol, 3-methyl-1-butanol, 2-methyl-1-butanol, 2,2-dimethyl-1-propanol, 3-pentanol, 2-pentanol, 3-methyl-2-butanol, or 2-methyl-2-butanol.

“Diethylene glycol” as used herein also refers to 1,5-dihydroxy-3-oxapentane, 2,2′-oxybis-ethanol, 2,2′-oxydiethanol, 2,2′-oxyethanol, 2-(2-hydroxyethoxy)ethanol, 2-hydroxyethoxyethanol, 3-oxapentamethylene-1,5-diol, 3-oxapentane-1,5-diol, bis(2-hydroxyethyl) ether, bis(β-hydroxyethyl) ether, ethylene diglycol and β,β′-dihydroxydiethyl ether.

“1,2-Ethanediol” (EDO) as used herein also refers to ethylene glycol, 1,2-dihydroxyethane, 1,2-ethylene glycol, 2-hydroxyethanol, ethylene alcohol, and ethylene dihydrate

“1,2-Propanediol” as used herein also refers to (RS)-1,2-propanediol, (±)-1,2-propanediol, (±)-Propylene glycol, 1,2-(RS)-propanediol, 1,2-dihydroxy-propane, 1,2-propylene glycol, 2,3-propanediol, 2-hydroxypropanol, DL-1,2-propanediol, dl-propylene glycol and α-propylene glycol.

“1,3-Propanediol” (PDO) as used herein also refers to 1,3-dihydroxypropane, 1,3-propylene glycol, 1,3-propylenediol, 2-deoxyglycerol, trimethylene glycol, β-propylene glycol and ω-propanediol.

“1,4-Butanediol” (BDO) as used herein also refers to 1,4-butylene glycol, 1,4-dihydroxybutane, 1,4-tetramethylene glycol, butylene glycol, tetramethylene 1,4-diol and tetramethylene glycol.

“2,3-Butanediol” as used herein also refers to 1,4-butylene glycol, 1,4-dihydroxybutane, 1,4-tetramethylene glycol, butylene glycol, tetramethylene 1,4-diol and tetramethylene glycol.

The term “alcohol equivalent” as used herein refers to the weight of alcohol that would be obtained by a perfect hydrolysis of an alcohol ester and the subsequent recovery of the alcohol from an amount of alcohol ester.

The term “aqueous phase titer” as used herein refers to the concentration of a particular alcohol (e.g., butanol) in the fermentation broth.

The term “effective titer” as used herein refers to the total amount of a particular alcohol (e.g., butanol) produced by fermentation or alcohol equivalent of the alcohol ester produced by alcohol esterification per liter of fermentation medium. For example, the effective titer of butanol in a unit volume of a fermentation includes: (i) the amount of butanol in the fermentation medium; (ii) the amount of butanol recovered from the organic extractant; (iii) the amount of butanol recovered from the gas phase, if gas stripping is used; and (iv) the alcohol equivalent of the butyl ester in either the organic or aqueous phase.

The term “effective rate” as used herein is the effective titer divided by the fermentation time.

The term “effective yield” as used herein is the total grams of product alcohol produced per gram of glucose consumed.

“In Situ Product Removal (ISPR)” as used herein means the selective removal of a specific fermentation product from a biological process such as fermentation, to control the product concentration in the biological process as the product is produced.

“Extractant” or “ISPR extractant” as used herein means an organic solvent used to extract any product alcohol such as butanol or used to extract any product alcohol ester produced by a catalyst from a product alcohol and a carboxylic acid or lipid. From time to time, as used herein the term “solvent” may be used synonymously with “extractant.” For the processes described herein, extractants are water-immiscible.

The terms “water-immiscible” or “insoluble” refer to a chemical component such as an extractant or solvent, which is incapable of mixing with an aqueous solution such as a fermentation broth, in such a manner as to form one liquid phase.

The term “aqueous phase” as used herein refers to the aqueous phase of a biphasic mixture obtained by contacting a fermentation broth with a water-immiscible organic extractant. In an embodiment of a process described herein that includes fermentative extraction, the term “fermentation broth” then specifically refers to the aqueous phase in biphasic fermentative extraction.

The term “organic phase” as used herein refers to the non-aqueous phase of a biphasic mixture obtained by contacting a fermentation broth with a water-immiscible organic extractant.

The term “carboxylic acid” as used herein refers to any organic compound with the general chemical formula —COOH in which a carbon atom is bonded to an oxygen atom by a double bond to make a carbonyl group (—C═O) and to a hydroxyl group (—OH) by a single bond. A carboxylic acid may be in the form of the protonated carboxylic acid, in the form of a salt of a carboxylic acid (e.g., an ammonium, sodium, or potassium salt), or as a mixture of protonated carboxylic acid and salt of a carboxylic acid. The term carboxylic acid may describe a single chemical species (e.g., oleic acid) or a mixture of carboxylic acids as can be produced, for example, by the hydrolysis of biomass-derived fatty acid esters or triglycerides, diglycerides, monoglycerides, and phospholipids.

The term “fatty acid” as used herein refers to a carboxylic acid (e.g., aliphatic monocarboxylic acid) having C₄ to C₂₈ carbon atoms (most commonly C₁₂ to C₂₄ carbon atoms), which is either saturated or unsaturated. Fatty acids may also be branched or unbranched. Fatty acids may be derived from, or contained in esterified form, in an animal or vegetable fat, oil, or wax. Fatty acids may occur naturally in the form of glycerides in fats and fatty oils or may be obtained by hydrolysis of fats or by synthesis. The term fatty acid may describe a single chemical species or a mixture of fatty acids. In addition, the term fatty acid also encompasses free fatty acids.

The term “fatty alcohol” as used herein refers to an alcohol having an aliphatic chain of C₄ to C₂₂ carbon atoms, which is either saturated or unsaturated.

The term “fatty aldehyde” as used herein refers to an aldehyde having an aliphatic chain of C₄ to C₂₂ carbon atoms, which is either saturated or unsaturated.

The term “fatty amide” as used herein refers to an amide having a long, aliphatic chain of C₄ to C₂₂ carbon atoms, which is either saturated or unsaturated

The term “fatty ester” as used herein refers to an ester having a long aliphatic chain of C₄ to C₂₂ carbon atoms, which is either saturated or unsaturated.

“Native oil” as used herein refers to lipids obtained from plants (e.g., biomass) or animals. “Plant-derived oil” as used herein refers to lipids obtain from plants in particular. From time to time, “lipids” may be used synonymously with “oil” and “acyl glycerides.” Native oils include, but are not limited to, tallow, corn, canola, capric/caprylic triglycerides, castor, coconut, cottonseed, fish, jojoba, lard, linseed, neetsfoot, oiticica, palm, peanut, rapeseed, rice, safflower, soya, sunflower, tung, jatropha, and vegetable oil blends.

The term “separation” as used herein is synonymous with “recovery” and refers to removing a chemical compound from an initial mixture to obtain the compound in greater purity or at a higher concentration than the purity or concentration of the compound in the initial mixture.

The term “butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 1-butanol, 2-butanol, or isobutanol.

The term “1-butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 1-butanol from acetyl-coenzyme A (acetyl-CoA).

The term “2-butanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce 2-butanol from pyruvate.

The term “isobutanol biosynthetic pathway” as used herein refers to an enzyme pathway to produce isobutanol from pyruvate.

The term “gene” refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene (i.e., it is modified from its native state or is from another source) comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign gene” or “heterologous gene” refers to a gene not normally found as a native gene in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism or chimeric genes.

As used herein the term “coding region” refers to a DNA sequence that codes for a specific amino acid sequence. “Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site, and stem-loop structure.

The term “codon-optimized” as it refers to genes or coding regions of nucleic acid molecules for transformation of various hosts, refers to the alteration of codons in the gene or coding regions of the nucleic acid molecules to reflect the typical codon usage of the host organism without altering the polypeptide encoded by the DNA. Codon optimization is within the ordinary skill in the art.

The term “polynucleotide” is intended to encompass a singular nucleic acid as well as plural nucleic acids, and refers to a nucleic acid molecule or construct, for example, messenger RNA (mRNA) or plasmid DNA (pDNA). As used herein, a “gene” is a polynucleotide. A polynucleotide can contain the nucleotide sequence of the full-length cDNA sequence or a fragment thereof, including the untranslated 5′ and 3′ sequences and the coding sequences. The polynucleotide can be composed of any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA (e.g., heterologous DNA). For example, polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. “Polynucleotide” embraces chemically, enzymatically, or metabolically modified forms.

A polynucleotide sequence may be referred to as “isolated,” in which it has been removed from its native environment. For example, a heterologous polynucleotide encoding a polypeptide or polypeptide fragment having dihydroxy-acid dehydratase activity contained in a vector is considered isolated for the purposes of the present invention. Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) polynucleotides in solution. Isolated polynucleotides or nucleic acids according to the present invention further include such molecules produced synthetically. An isolated polynucleotide fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, or synthetic DNA.

As used herein, the term “polypeptide” is intended to encompass a singular “polypeptide” as well as plural “polypeptides,” and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds). The term “polypeptide” refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, peptides, dipeptides, tripeptides, oligopeptides, “protein,” “amino acid chain,” or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide,” and the term “polypeptide” may be used instead of, or interchangeably with any of these terms. A polypeptide may be derived from a natural biological source or produced by recombinant technology, but is not necessarily translated from a designated nucleic acid sequence. It may be generated in any manner including by chemical synthesis.

By an “isolated” polypeptide or a fragment, variant, or derivative thereof is intended a polypeptide that is not in its natural milieu. No particular level of purification is required. For example, an isolated polypeptide can be removed from its native or natural environment. Recombinantly produced polypeptides and proteins expressed in host cells are considered isolated for purposes of the invention, as are native or recombinant polypeptides which have been separated, fractionated, or partially or substantially purified by any suitable technique.

As used herein, “recombinant microorganism” refers to microorganisms such as bacteria or yeast, that are modified by use of recombinant DNA techniques, for example, by engineering a host cell to comprise a biosynthetic pathway such as a biosynthetic pathway to produce an alcohol such as butanol.

The present invention satisfies the need for alternative extractive fermentation methods which do not necessitate the partitioning of the product alcohol between the fermentation medium and the ISPR extractant as a means to reduce the toxic effect of the product alcohol (such as butanol) on the microorganism. It also satisfies the need to reduce the degradation of the partition coefficient of a fermentation product ISPR extractant by providing methods for producing alcohol such as butanol in which the product alcohol is converted into alcohol esters which can be less toxic to the microorganism and where there is realized a concomitant reduction in the degradation of the partition coefficient of a fermentation product extractant, resulting in improved production yields of alcohol (as a combination of free alcohol and alcohol esters that can be converted back to alcohol after separation from the fermentation medium). Moreover, the present invention offers solutions to disadvantages of alternative alcohol product removal processes such that the methods herein can be combined with existing processes (e.g., solids removal) to provide increased product removal at economic and environmental advantage. As such, the present invention provides further related advantages, as will be made apparent by the description of the embodiments that follow.

The present invention provides methods for removing alcohol from a fermentation medium by esterifying the alcohol with carboxylic acid and extracting the resulting alcohol ester from the fermentation medium, whereafter the alcohol can be recovered from the alcohol ester. The acid may be added to the fermentation medium directly as free fatty acid or may be derived from oil. The present invention also provides methods for removing or reducing oil from an alcohol fermentation process by hydrolyzing the oil derived from a feedstock into carboxylic acid which can be used for the esterification of alcohol and/or serve as an ISPR extractant or a component of the ISPR extractant for extracting the alcohol ester.

Decreasing the amount of water present in a reaction system, or employing a reaction system that uses only one or more non-aqueous solvents, has typically been necessary for esterification of alcohols by carboxylic acids when catalyzed by enzymes such as lipases. Described herein is the surprising finding that lipase enzymes can efficiently catalyze the esterification of a product alcohol with a carboxylic acid during fermentation of a fermentable carbon source to produce product alcohol. Also described herein is the surprising finding that esterification of a product alcohol with a carboxylic acid during a fermentation can provide improvements in the fermentation performance. For example, by capturing the product alcohol (e.g., butanol) as produced in ester form it effectively reduces the concentration of the product alcohol in the aqueous phase and thus, mitigates the toxic effects of the product alcohol on glucose consumption and product production. The present invention will be described with reference to the Figures. FIG. 1 illustrates an exemplary process flow diagram for production of fermentative alcohol such as ethanol or butanol, according to an embodiment of the present invention. As shown, a feedstock 12 can be introduced to an inlet in a liquefaction vessel 10 and liquefied to produce a feedstock slurry 16. Feedstock 12 contains hydrolysable polysaccharides that supplies a fermentable carbon substrate (e.g., fermentable sugar such as glucose), and can be a biomass such as, but not limited to, rye, wheat, cane or corn, or can otherwise be derived from a biomass. In some embodiments, feedstock 12 can be one or more components of a fractionated biomass, and in other embodiments, feedstock 12 can be a milled, unfractionated biomass. In some embodiments, feedstock 12 can be corn, such as dry milled, unfractionated corn kernels, and the undissolved particles can include germ, fiber, and gluten. The undissolved solids are non-fermentable portions of feedstock 12. For purposes of the discussion herein with reference to the embodiments shown in the Figures, feedstock 12 will often be described as constituting milled, unfractionated corn in which the undissolved solids have not been separated therefrom. However, it should be understood that the exemplary methods and systems described herein can be modified for different feedstocks whether fractionated or not, as apparent to one of skill in the art. Furthermore, as one skilled in the art can appreciate, maximizing feedstock content (e.g., corn content) can maximize sugar content as well as product titer. In some embodiments, feedstock 12 can be high-oleic corn, such that corn oil derived therefrom is a high-oleic corn oil having an oleic acid content of at least about 55 wt % oleic acid. In some embodiments, the oleic acid content in high-oleic corn oil can be up to about 65 wt %, as compared with the oleic acid content in normal corn oil which is about 24 wt %. High-oleic oil can provide some advantages for use in the methods of the present invention, as hydrolysis of the oil provides free fatty acids having a high oleic acid content for contacting with a fermentation broth.

The process of liquefying feedstock 12 involves hydrolysis of polysaccharides in feedstock 12 into sugars including, for example, dextrins and oligosaccharides, and is a conventional process. Any known liquefying processes as well as the corresponding liquefaction vessel, normally utilized by the industry can be used including, but not limited to, the acid process, the acid-enzyme process, or the enzyme process. Such processes can be used alone or in combination. In some embodiments, the enzyme process can be utilized and an appropriate enzyme 14, for example, alpha-amylase, is introduced to an inlet in liquefaction vessel 10. Water can also be introduced to liquefaction vessel 10. In some embodiments, a saccharification enzyme, for example, glucoamylase, may also be introduced to liquefaction vessel 10. In additional embodiments, a lipase may also be introduced to liquefaction vessel 10 to catalyze the conversion of one or more components of the oil to free fatty acids.

Feedstock slurry 16 produced from liquefying feedstock 12 comprises fermentable carbon substrate (e.g., sugar), oil, and undissolved solids derived from the feedstock. Feedstock slurry 16 can be discharged from an outlet of liquefaction vessel 10. In some embodiments, feedstock 12 is corn or corn kernels and therefore, feedstock slurry 16 is a corn mash slurry. In some embodiments, feedstock 12 is a lignocellulosic feedstock and therefore, feedstock slurry 16 may be a lignocellulosic hydrolysate. In some embodiments, feedstock 12 is sugar cane.

Feedstock slurry 16 is introduced into a fermentation vessel 30 along with a microorganism 32. Fermentation vessel 30 is configured to ferment slurry 16 to produce alcohol. In particular, microorganism 32 metabolizes the fermentable sugar in slurry 16 and excretes a product alcohol. Microorganism 32 is selected from the group of bacteria, cyanobacteria, filamentous fungi, and yeasts. In some embodiments, microorganism 32 can be a bacteria such as E. coli. In some embodiments, microorganism 32 can be a fermentative recombinant microorganism. The slurry can include sugar, for example, in the form of oligosaccharides, and water, and in some embodiments, can comprise less than about 20 g/L of monomeric glucose, less than about 10 g/L, or less than about 5 g/L of monomeric glucose. Suitable methodology to determine the amount of monomeric glucose is well known in the art. Such suitable methods known in the art include HPLC.

In some embodiments, slurry 16 is subjected to a saccharification process in order to break the complex sugars (e.g., oligosaccharides) in slurry 16 into monosaccharides that can be readily metabolized by microorganism 32. Any known saccharification process, normally utilized by the industry can be used including, but not limited to, the acid process, the acid-enzyme process, or the enzyme process. In some embodiments, simultaneous saccharification and fermentation (SSF) can occur inside fermentation vessel 30 as shown in FIG. 1. In some embodiments, an enzyme 38 such as glucoamylase, can be introduced to an inlet in fermentation vessel 30 in order to breakdown the starch or oligosaccharides to glucose capable of being metabolized by microorganism 32.

Carboxylic acid 28 and/or native oil 26 are introduced into fermentation vessel 30, along with a catalyst 42. Catalyst 42 can be introduced before, after, or contemporaneously with enzyme 38. Thus, in some embodiments, addition of enzyme 38 and catalyst 42 can be stepwise (e.g., catalyst 42, then enzyme 38, or vice versa) or substantially simultaneous (i.e., at exactly the same time as in the time it takes for a person or a machine to perform the addition in one stroke, or one enzyme/catalyst immediately following the other catalyst/enzyme as in the time it takes for a person or a machine to perform the addition in two strokes). Catalyst 42 is capable of esterifying the product alcohol with carboxylic acid 28 to form an alcohol ester. For example, in the case of butanol production, catalyst 42 is capable of esterifying butanol with carboxylic acid 28 to form a butyl ester.

In the instance that native oil 26 is supplied to fermentation vessel 30, at least a portion of the acyl glycerides in oil 26 can be hydrolyzed to carboxylic acid 28 by contacting oil 26 with catalyst 42. The resulting acid/oil composition from hydrolyzing oil 26 is typically at least about 17 wt % carboxylic acid 28 (as free fatty acids). In some embodiments, the resulting acid/oil composition from hydrolyzing oil 26 is at least about 20 wt % carboxylic acid, at least about 25 wt % carboxylic acid, at least about 30 wt % carboxylic acid, at least about 35 wt % carboxylic acid, at least about 40 wt % carboxylic acid, at least about 45 wt % carboxylic acid, at least about 50 wt % carboxylic acid, at least about 55 wt % carboxylic acid, at least about 60 wt % carboxylic acid, at least about 65 wt % carboxylic acid, at least about 70 wt % carboxylic acid, at least about 75 wt % carboxylic acid, at least about 80 wt % carboxylic acid, at least about 85 wt % carboxylic acid, at least about 90 wt % carboxylic acid, at least about 95 wt % carboxylic acid, or at least about 99 wt % carboxylic acid. In some embodiments, the resulting acid/oil composition includes monoglycerides and/or diglycerides from the partial hydrolysis of the acyl glycerides in the oil. In some embodiments, the resulting acid/oil composition includes glycerol, a by-product of acyl glyceride hydrolysis. In some additional embodiments, the resulting acid/oil composition includes lysophospholipids from the partial hydrolysis of phospholipids in the oil.

In some embodiments, after hydrolysis of the acyl glycerides in oil 26, the remaining acyl glycerides from oil 26 are from about 0 wt % to at least about 2 wt % of the fermentation broth composition. In some additional embodiments, after hydrolysis of the acyl glycerides in oil 26, the remaining acyl glycerides from oil 26 are at least about 0.5 wt % of the fermentation broth composition. Thus, in some embodiments, the acyl glycerides from oil 26 can be catalytically hydrolyzed to carboxylic acid 28 using catalyst 42, and catalyst 42 can also esterify carboxylic acid 28 with the product alcohol. In some embodiments, a second catalyst (not shown) can be introduced to the fermentation vessel for hydrolysis of the acyl glycerides. In addition, the acyl glycerides in the oil derived from feedstock 12 and present in slurry 16 can also be hydrolyzed to carboxylic acid 28′ (see, e.g., the embodiment of FIG. 3). In some embodiments, the concentration of the carboxylic acid (such as fatty acid) in the fermentation vessel exceeds the solubility limit in the aqueous phase and results in the production a two-phase fermentation mixture comprising an organic phase and an aqueous phase. In some embodiments, the concentration of carboxylic acids in the fermentation broth is typically not greater than about 0.8 g/L and is limited by the solubility of the carboxylic acid in the broth. In some embodiments, catalyst 42 and the second catalyst, if used, can be one or more enzymes, for example, lipase enzymes. In some embodiments, catalyst 42 can be one or more enzymes, for example, hydrolase enzymes such as lipase enzymes. Lipase enzymes used may be derived from any source including, for example, Absidia, Achromobacter, Aeromonas, Alcaligenes, Alternaria, Aspergillus, Achromobacter, Aureobasidium, Bacillus, Beauveria, Brochothrix, Candida, Chromobacter, Coprinus, Fusarium, Geotricum, Hansenula, Humicola, Hyphozyma, Lactobacillus, Metarhizium, Mucor, Nectria, Neurospora, Paecilomyces, Penicillium, Pseudomonas, Rhizoctonia, Rhizomucor, Rhizopus, Rhodosporidium, Rhodotorula, Saccharomyces, Sus, Sporobolomyces, Thermomyces, Thiarosporella, Trichoderma, Verticillium, and/or a strain of Yarrowia. In a preferred aspect, the source of the lipase is selected from the group consisting of Absidia blakesleena, Absidia corymbifera, Achromobacter iophagus, Alcaligenes sp., Alternaria brassiciola, Aspergillus flavus, Aspergillus niger, Aspergillus tubingensis, Aureobasidium pullulans, Bacillus coagulans, Bacillus pumilus, Bacillus strearothermophilus, Bacillus subtilis, Brochothrix thermosohata, Candida cylindracea (Candida rugosa), Candida paralipolytica, Candida antarctica lipase A, Candida antarctica lipase B, Candida emobii, Candida deformans, Chromobacter viscosum, Coprinus cinerius, Fusarium oxysporum, Fusarium solani, Fusarium solani pisi, Fusarium roseum culmorum, Geotricum penicillatum, Hansenula anomala, Humicola brevispora, Humicola brevis var. thermoidea, Humicola insolens, Lactobacillus curvatus, Rhizopus oryzae, Penicillium cyclopium, Penicillium crustosum, Penicillium expansum, Penicillium sp. I, Penicillium sp. II, Pseudomonas aeruginosa, Pseudomonas alcaligenes, Pseudomonas cepacia (syn. Burkholderia cepacia), Pseudomonas fluorescens, Pseudomonas fragi, Pseudomonas maltophilia, Pseudomonas mendocina, Pseudomonas mephitica lipolytica, Pseudomonas alcaligenes, Pseudomonas plantari, Pseudomonas pseudoalcaligenes, Pseudomonas putida, Pseudomonas stutzeri, and Pseudomonas wisconsinensis, Rhizoctonia solani, Rhizomucor miehei, Rhizopus japonicus, Rhizopus microsporus, Rhizopus nodosus, Rhodosporidium toruloides, Rhodotorula glutinis, Saccharomyces cerevisiae, Sporobolomyces shibatanus, Sus scrofa, Thermomyces lanuginosus (formerly Humicola lanuginose), Thiarosporella phaseolina, Trichoderma harzianum, Trichoderma reesei, and Yarrowia lipolytica. In a further preferred aspect, the lipase is selected from the group consisting of Thermomcyces lanuginosus lipase, Aspergillus sp. lipase, Aspergillus niger lipase, Aspergillus tubingensis lipase, Candida antarctica lipase B, Pseudomonas sp. lipase, Penicillium roqueforti lipase, Penicillium camembertii lipase, Mucor javanicus lipase, Burkholderia cepacia lipase, Alcaligenes sp. lipase, Candida rugosa lipase, Candida parapsilosis lipase, Candida deformans lipase, lipases A and B from Geotrichum candidum, Neurospora crassa lipase, Nectria haematococca lipase, Fusarium heterosporum lipase Rhizopus delemar lipase, Rhizomucor miehei lipase, Rhizopus arrhizus lipase, and Rhizopus oryzae lipase. Suitable commercial lipase preparations suitable as catalyst 42 include, but are not limited to, Lipolase® 100 L, Lipex® 100L, Lipoclean® 2000T, Lipozyme® CALB L, Novozyme® CALA L, and Palatase 20000L, available from Novozymes, or from Pseudomonas fluorescens, Pseudomonas cepacia, Mucor miehei, hog pancreas, Candida cylindracea, Candida rugosa, Rhizopus niveus, Candida antarctica, Rhizopus arrhizus or Aspergillus available from SigmaAldrich. In one embodiment, the lipase may be thermostable and/or thermotolerant, and/or solvent tolerant.

Phospholipases are enzymes that hydrolyze the ester bonds of phospholipids, but many phospholipases also can hydrolyze triglycerides, diglycerides, and monoglycerides (lipid acyl hydrolase (LAH) activity). As used herein, the term “phospholipase” encompasses enzymes having any phospholipase activity, for example, cleaving a glycerolphosphate ester linkage (catalyzing hydrolysis of a glycerolphosphate ester linkage), for example, in an oil, such as a crude oil or a vegetable oil. The phospholipase activity of the invention can generate a water extractable phosphorylated base and a diglyceride. The phospholipase activity can comprise a phospholipase C (PLC) activity; a PI-PLC activity, a phospholipase A (PLA) activity such as a phospholipase A1 or phospholipase A2 activity; a phospholipase B (PLB) activity such as a phospholipase B1 or phospholipase B2 activity, including lysophospholipase (LPL) activity and/or lysophospholipase-transacylase (LPT A) activity; a phospholipase D (PLD) activity such as a phospholipase DI or a phospholipase D2 activity; and/or a patatin activity or any combination thereof.

The term “phospholipase” also encompasses enzymes having lysophospholipase activity, where the two substrates of this enzyme are 2-lysophosphatidylcholine and H₂O, and where its two products are glycerophosphocholine and carboxylate. Phospholipase A1 (PLA1) enzymes remove the 1-position fatty acid to produce free fatty acid and 1-lyso-2-acylphospholipid. Phospholipase A2 (PLA2) enzymes remove the 2-position fatty acid to produce free fatty acid and l-acyl-2-lysophospholipid. PLA1 and PLA2 enzymes can be intra- or extra-cellular, membrane-bound or soluble. Phospholipase C (PLC) enzymes remove the phosphate moiety to produce 1,2 diacylglycerol and a phosphate ester. Phospholipase D (PLD) enzymes produce 1,2-diacylglycerophosphate and base group. A phospholipase useful in the present invention may be obtained from a variety of biological sources, for example, but not limited to, filamentous fungal species within the genus Fusarium, such as a strain of F. culmorum, F. heterosporum, F. solani, or F. oxysporum; or a filamentous fungal species within the genus Aspergillus, such as a strain of Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus, Aspergillus niger or Aspergillus oryzae. Also useful in the present invention are Thermomyces lanuginosus phospholipase variants such as the commercial product Lecitase® Ultra (Novozymes A'S, Denmark). One or more phospholipases may be applied as lyophilized powder, immobilized or in aqueous solution.

An alcohol (e.g., butanol, 1,3-propanediol, 1,4-butanediol) that is produced by fermentation of one or more fermentable sugars may be converted to a carboxylic acid ester by an enzyme-catalyzed reaction where the carboxylic acid is esterified with the alcohol. Enzymes such as lipase, phospholipase, and lysophospholipase may catalyzed this reaction; however, these enzymes may be inactivated due to one or more factors including, but not limited to, hydrodynamic shear or inactivation at gas-liquid and liquid-liquid interfaces. In fermentations where oligosaccharides are additionally converted to one or more fermentable sugars, the enzyme that converts oligosaccharides to fermentable sugars (e.g., glucoamylase) may also be inactivated by one or more of these same factors.

Inactivation of enzymes at a gas-liquid interface (e.g., may occur at the interface of bubbles with the fermentation broth) that results from aeration of the fermentation broth and/or is produced by the evolution of gaseous carbon dioxide in the broth during fermentation of one or more fermentable sugars, is well-known in the art. Inactivation of Hen egg white lysozyme and Thermomyces lanuginosus lipase produced in Aspergillus oryzae (Novozymes Lipolase®) was observed at the gas-liquid interface in three different reactor configurations: bubble column, stirred vessel with baffles (with no aeration by gas sparging), and falling film (Ghadge, et al., Chem. Eng. Sci. 58:5125-5134, 2003). The mechanism of inactivation of Thermomyces lanuginosus lipase (produced in Aspergillus oryzae; Novozymes Lipolase 100L®) at the gas-liquid interface in a baffled stirred-tank reactor (with no aeration by gas sparging) has been reported (Patil, et al., AIChE J. 46:1280-1283, 2000).

Stahmann, et al. (Eur. J. Biochem. 244:220-225, 1997) have reported that Ashbya gossypii lipase was inactivated within minutes in stirred gas/water, trioleoylglycerol/water or oleic acid/water mixtures, due to interfacial inactivation at either a gas/liquid or liquid/liquid interface. Elias, et al. (Adv. Biochem. Engineering/Biotechnology 59:47-71, 1998) have reported that: (i) some enzymes are inactivated by hydrodynamic shear even in the absence of a gas-liquid interface; (ii) for enzymes that are inactivated by hydrodynamic shear, the rate of inactivation increases in the presence of gas-liquid interface; (iii) some enzymes are not inactivated in the absence of gas-liquid interface regardless of the applied hydrodynamic shear; and (iv) for enzymes that require a gas-liquid interface for inactivation, the rate of inactivation increases with an increase in hydrodynamic shear. Ross, et al. (J. Mol. Catal. B: Enzymatic 8:183-192, 2000) have described the interfacial inactivation of α-chymotrypsin, β-chymotrypsin, papain, and pig liver esterase in a variety of aqueous/organic solvent mixtures by passing solvent droplets up through an aqueous enzyme solution in a bubble column apparatus. The kinetics and mechanism of shear inactivation of Candida cylindracea lipase in a stirred tank reactor has also been reported, where the mechanism of inactivation was found to be due to a shear-induced gas-liquid interface effect (Lee, et al., Biotechnol. Bioeng. 33:183-190, 1989).

Under the fermentation conditions employed in some methods described herein, hydrodynamic shear and gas-liquid and liquid-liquid interfaces are each present over the course of the fermentation, and capable of causing enzyme inactivation. The potential effect of each of these factors on the stability and activity of one or more of the enzymes (e.g., glucoamylase, lipase, phospholipase, and lysophospholipase) present in the two-phase mixture (e.g., fermentation broth and carboxylic acid) during fermentation under the conditions described herein could not have been anticipated based on the prior art. Although each of these factors could have resulted in the inactivation of one or more enzymes in the fermentation mixture, sufficient enzyme activity to catalyze esterification of the product alcohol by carboxylic acid to produce carboxylic acid esters was maintained over the course of the fermentation. In reactions where glucoamylase was also present in the two-phase fermentation mixture of fermentation broth and carboxylic acid, sufficient enzyme activity (i.e., to convert oligosaccharide to fermentable sugars) was also maintained.

Carboxylic acid 28 can be any carboxylic acid capable of esterifying with a product alcohol such as butanol or ethanol, to produce an alcohol ester of the carboxylic acid. For example, in some embodiments, carboxylic acid 28 can be free fatty acid, and in some embodiments, the carboxylic acid or free fatty acid has 4 to 28 carbons, 4 to 22 carbons in other embodiments, 8 to 22 carbons in other embodiments, 10 to 28 carbons in other embodiments, 7 to 22 carbons in other embodiments, 12 to 22 carbons in other embodiments, 4 to 18 carbons in other embodiments, 12 to 22 carbons in other embodiments, and 12 to 18 carbons in still other embodiments. In some embodiments, carboxylic acid 28 is one or more of the following fatty acids: azaleic, capric, caprylic, castor, coconut (i.e., as a naturally-occurring combination of fatty acids including lauric, myrisitic, palmitic, caprylic, capric, stearic, caproic, arachidic, oleic, and linoleic, for example), isostearic, lauric, linseed, myristic, oleic, palm oil, palmitic, palm kernel, pelargonic, ricinoleic, sebacic, soya, stearic acid, tall oil, tallow, and #12 hydroxy stearic. In some embodiments, carboxylic acid 28 is one or more of diacids.

In some embodiments, carboxylic acid 28 can be a mixture of two or more different fatty acids. In some embodiments, carboxylic acid 28 comprises free fatty acid derived from hydrolysis of acyl glycerides by any method known in the art including chemical or enzymatic hydrolysis. In some embodiments as noted above, carboxylic acid 28 can be derived from native oil 26 by enzymatic hydrolysis of the oil glycerides using an enzyme as catalyst 42. In some embodiments, the fatty acids or mixtures thereof comprise unsaturated fatty acids. The presence of unsaturated fatty acids decreases the melting point, providing advantages for handling. Of the unsaturated fatty acids, those which are monounsaturated, that is, possessing a single carbon-carbon double bond, may provide advantages with respect to melting point without sacrificing suitable thermal and oxidative stability for process considerations. In some embodiments, stabilizers may be utilized to mitigate the degradation of carboxylic acid(s).

In some embodiments, native oil 26 can be tallow, corn, canola, capric/caprylic triglycerides, castor, coconut, cottonseed, fish, jojoba, lard, linseed, neetsfoot, oiticica, palm, peanut, rapeseed, rice, safflower, soya, sunflower, tung, jatropha, pumpkin, grape seed, and vegetable oil blends (or oils that can be purified into higher concentrations of different chain length and levels of unsaturation (i.e., 18:1)). In some embodiments, native oil 26 is a mixture of two or more native oils such as a mixture of palm and soybean oils, for example. In some embodiments, native oil 26 is a plant-derived oil. In some embodiments, the plant-derived oil can be, though not necessarily, derived from biomass that can be used in a fermentation process. The biomass can be the same or different source from which feedstock 12 is obtained. Thus, for example, in some embodiments, oil 26 can be derived from corn, whereas feedstock 12 can be cane. For example, in some embodiments, oil 26 can be derived from corn, and the biomass source of feedstock 12 is also corn. Any possible combination of different biomass sources for oil 26 versus feedstock 12 can be used, as should be apparent to one of skill in the art. In some embodiments, oil 26 is derived from the biomass used in the fermentation process. Thus, in some embodiments, as later described with reference to FIG. 3, oil 26 is derived directly from feedstock 12 as oil 26′. For example, when feedstock 12 is corn, then oil 26′ is the feedstock's constituent corn oil.

In other embodiments, carboxylic acid 28 may comprise one or more of the following carboxylic acids: formic acid, acetic acid, lactic acid, propionic acid, butyric acid, valeric acid, caproic acid, oxalic acid, malonic acid, malic acid, succinic acid, maleic acid, fumaric acid, tartaric acid, oxaloacetic acid, citric acid, benzoic acid, salicyclic acid, toluic acid, phthalic acid as well as other dicarboxylic acids, tricarboxylic acids, and aromatic carboxylic acids, and mixtures thereof. In one embodiment, the concentration of the one or more carboxylic acids is in a range or ranges that are biocompatible with microorganism 32. In another embodiment, the concentration of the one or more carboxylic acids is in a range or ranges that are compatible with catalyst(s) and/or enzyme(s) of the claimed methods.

Optionally, ethanol 33 may be supplied to fermentation vessel 30 to be included in the fermentation broth. In some embodiments, when a recombinant microorganism having a butanol biosynthetic pathway and/or reduced or eliminated expression of pyruvate decarboxylase is used as microorganism 32, microorganism 32 may require supplementation of a 2-carbon substrate, for example, ethanol, for survival and growth. Thus, in some embodiments, ethanol 33 may be supplied to fermentation vessel 30.

However, it has been surprisingly found that methods of the present invention, in which carboxylic acid such as fatty acid, is present in the fermentation vessel, can allow reduction of the amount of ethanol 33 typically supplied for a given recombinant microorganism without detriment to the vitality of the recombinant microorganism. Further, in some embodiments of the methods of the present invention, the alcohol (e.g., butanol) production rate without ethanol supplementation can be comparable with the production rate that can be realized when ethanol 33 is supplemented. As further demonstrated by the comparative examples presented in the Examples 1-14 below, the butanol production rate when fatty acid but not ethanol is in the fermentation vessel can be comparable to or greater than the butanol production rate when neither fatty acid nor ethanol is in the fermentation vessel. Thus, in some embodiments, the amount of ethanol 33 supplementation is reduced compared to conventional processes. For example, a typical amount of ethanol added to a fermentation vessel for microorganisms requiring supplementation of a 2-carbon substrate is about 5 g/L anhydrous ethanol (i.e., 5 g anhydrous ethanol per liter of fermentation medium). In some embodiments, the fermentation is not supplemented with any ethanol 33. In the latter case, the stream of ethanol 33 is entirely omitted from the fermentation vessel. Thus, in some embodiments of the present invention, it is possible to reduce or eliminate the cost associated with supplemental ethanol 33, as well as the inconvenience associated with storing vats of ethanol 33 and supplying it to the fermentation vessel during butanol fermentation or other alcohol fermentation that employs a microorganism that may require supplementation of a 2-carbon substrate to survive and grow.

Moreover, regardless of ethanol supplementation, in some embodiments, the methods of the present invention can provide a higher rate of glucose uptake by microorganism 32 by virtue of the presence of fatty acids during the fermentation. The fatty acids can be introduced into fermentation vessel 30 as carboxylic acid 28, hydrolyzed from supplied oil 26, and/or derived from hydrolysis of constituent biomass oil of slurry 16. Methods for producing a product alcohol from a fermentation process in which free fatty acids are produced at a step in the process and are contacted with microorganism cultures in a fermentation vessel for improving microorganism growth rate and glucose consumption are described in co-pending, commonly owned U.S. Provisional Application Ser. No. 61/368,451, filed on Jul. 28, 2010, which is incorporated herein in its entirety by reference thereto.

In fermentation vessel 30, alcohol produced by microorganism 32 is esterified with carboxylic acid 28 using catalyst 42 to form alcohol esters. For example, in the case of butanol production, butanol produced by microorganism 32 is esterified with carboxylic acid 28 using catalyst 42 to form butyl esters. In situ product removal (ISPR) can be utilized to remove the alcohol esters from the fermentation broth. As demonstrated herein, using catalyst to form esters in conjunction with ISPR can improve the performance of the fermentation. In some embodiments, using catalyst to form esters in conjunction with ISPR (such as, for example, liquid-liquid extraction) can increase the effective titer by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 100% as compared to the effective titer in an analogous fermentation using ISPR without a catalyst forming esters. Similarly, in some embodiments, using a catalyst to form esters in conjunction with ISPR (such as, for example, liquid-liquid extraction) can increase the effective rate by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 100% as compared to the effective rate in an analogous fermentation using ISPR without a catalyst forming esters (see, e.g., Examples 9 and 11-14, Table 3). In some embodiments, the effective yield is increased by at least about 10%, at least about 20%, at least about 30%, at least about 40%, or at least about 50%. In some embodiments, the resulting fermentation broth after alcohol esterification can comprise free (i.e., unesterified) alcohol and in some embodiments, the concentration of free alcohol in the fermentation broth after alcohol esterification is not greater than 1, 3, 6, 10, 15, 20, 25, 30 25, 40, 45, 50, 55, or 60 g/L when the product alcohol is butanol, or when the product alcohol is ethanol, the concentration of free alcohol in the fermentation broth after alcohol esterification is not greater than 15, 20, 25, 30 25, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 g/L. In some embodiments, the ratio of alcohol ester to alcohol in the fermentation vessel may be about 1:1. In some embodiments, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% of the effective titer of alcohol is converted to alcohol ester.

In some embodiments, a grain load on water at a sufficient concentration to achieve a final effective titer of at least about 50 g/L, at least about 75 g/L, or at least about 100 g/L may be used in a grain mash fermentation comprising a microorganism capable of producing an alcohol such as butanol. In other embodiments, the grain mash fermentation may use simultaneous saccharification and fermentation (SSF), and the concentration of glucose may remain relatively low, for example, at least about 75 g/L glucose in the fermentation broth phase over the course of the fermentation. In some embodiments, fatty acids may be added to the fermentor in an amount that is less than about 70% of the volume of the fermentor, less than about 50% of the volume of the fermentor, or less than about 30% of the volume of the fermentor. The amount of fatty acid added to the fermentor may be a means to maintain the aqueous phase titer of butanol during fermentation. In other embodiments, the aqueous phase titer of butanol may be maintained at a level less than about 35 g/L of fermentation broth, less than about 25 g/L of fermentation broth, or less than about 20 g/L of fermentation broth. In other embodiments, the amount of active esterification enzyme in the fermentation broth may be less than about 100 ppm, less than about 50 ppm, or less than about 10 ppm active enzyme. In some embodiments, the cell mass employed in a fermentation broth may be less than about 50 g dcw/L, less than about 20 g dcw/L, or less than about 10 g dcw/L. In other embodiments, the fermentation process may run at least about 30 hours to at least about 100 hours, at least about 40 hours to at least about 80 hours, or at least about 50 hours to at least about 70 hours.

In some embodiments, a brix on water at a sufficient concentration to achieve a final effective titer of at least about 30 g of butanol per liter of fermentation broth phase, at least about 45 g of butanol per liter of fermentation broth phase, or at least about 60 g of butanol per liter of fermentation broth phase may be used in a sugarcane fermentation comprising a microorganism capable of producing butanol. In some embodiments, fatty acids may be added to the fermentor in an amount that is less than about 70% of the volume of the fermentor, less than about 50% of the volume of the fermentor, or less than about 30% of the volume of the fermentor. The amount of fatty acid added to the fermentor may be a means to maintain the aqueous phase titer of butanol during fermentation. In other embodiments, the aqueous phase titer of butanol may be maintained at a level less than about 35 g/L of fermentation broth, less than about 25 g/L of fermentation broth, or less than about 15 g/L of fermentation broth. In other embodiments, the amount of active esterification enzyme in the fermentation broth may be less than about 200 ppm, less than about 100 ppm, or less than about 20 ppm active enzyme. In some embodiments, the cell mass employed in a fermentation broth may initially be at least about 100 g of cell per liter of broth in the initial charge occupying at least about 30% of the fermentor volume. After 3-7 hours of fermentation, the cell mass may be diluted to at least about 25 g of cell per liter of fermentation broth by the addition of a sugarcane feed. The cells may continue to grow to at least about 30 g of cell per liter of fermentation broth over the 8 to 15 hours of total fermentation time. In some embodiments, the fermentation broth is contacted during fermentation with an extractant to form a two-phase mixture comprising an aqueous phase and an organic phase. In such embodiments, ISPR including liquid-liquid extraction may be conveniently carried out. Liquid-liquid extraction can be performed according to the processes described in U.S. Patent Application Publication No. 2009/0305370, the disclosure of which is hereby incorporated in its entirety. U.S. Patent Application Publication No. 2009/0305370 describes methods for producing and recovering butanol from a fermentation broth using liquid-liquid extraction, the methods comprising the step of contacting the fermentation broth with a water-immiscible extractant to form a two-phase mixture comprising an aqueous phase and an organic phase. Typically, the extractant can be an organic extractant selected from the group consisting of saturated, mono-unsaturated, poly-unsaturated (and mixtures thereof) C₁₂ to C₂₂ fatty alcohols, C₁₂ to C₂₂ fatty acids, esters of C₁₂ to C₂₂ fatty acids, C₁₂ to C₂₂ fatty aldehydes, C₁₂ to C₂₂ fatty amides, and mixtures thereof. The extractant may also be an organic extractant selected from the group consisting of saturated, mono-unsaturated, poly-unsaturated (and mixtures thereof) C₄ to C₂₂ fatty alcohols, C₄ to C₂₈ fatty acids, esters of C₄ to C₂₈ fatty acids, C₄ to C₂₂ fatty aldehydes, and mixtures thereof. For use with the processes described herein, the extractant(s) for ISPR are typically non-alcohol extractants, so as to avoid consuming carboxylic acid 28 in fermentation vessel 30 by catalytic esterification of carboxylic acid 28 with an alcohol extractant, whereby less carboxylic acid would be available for esterification with the product alcohol. For example, if oleyl alcohol is used as an ISPR extractant, then oleyl alcohol esters of the carboxylic acid can be produced in fermentation vessel due to the presence of active catalyst 42, as further demonstrated in the Example 24 below.

With reference to the embodiment of FIG. 1, the carboxylic acid 28 can also serve as an ISPR extractant 28 or a component thereof. As earlier noted, carboxylic acid 28 can be supplied, and/or formed in situ in the case when native oil 26 is supplied to fermentation vessel 30, and/or formed in situ in the case when feedstock 16 includes oil that can be hydrolyzed. In some embodiments, ISPR extractant 28 includes free fatty acids. In some embodiments, ISPR extractant 28 includes corn oil fatty acids (COFA). In some embodiments, oil 26 is corn oil, whereby ISPR extractant 28 is COFA. In some embodiment, COFA may be pretreated to remove degradation products (e.g., hydrogenation, distillation, and/or urea treatment to remove saturated acids). COFA may be ISPR extractant (carboxylic acid) 28 contacts the fermentation broth and forms a two-phase mixture comprising an aqueous phase 34 and an organic phase. The product alcohol ester formed in the fermentation vessel preferentially partitions into the organic phase to form an ester-containing organic phase 36. That is, the product alcohol esters are produced at a concentration in excess of the equilibrium concentration of alcohol ester present in the aqueous phase 34 and therefore, preferentially partition into the organic phase. Any free product alcohol in the fermentation broth also preferentially partitions into the ester-containing organic phase. The biphasic mixture can be removed from fermentation vessel 30 as stream 39 and introduced into a vessel 35, in which the ester-containing organic phase 36 is separated from aqueous phase 34. Separation of biphasic mixture 39 into ester-containing organic phase 36 and aqueous phase 34 can be achieved using any methods known in the art, including but not limited to, siphoning, aspiration, decantation, centrifugation, using a gravity settler, membrane-assisted phase splitting, hydroclyclone, and the like. All or part of aqueous phase 34 can be recycled into fermentation vessel 30 as fermentation medium (as shown), or otherwise discarded and replaced with fresh medium, or treated for the removal of any remaining product alcohol and then recycled to fermentation vessel 30.

With reference to FIG. 1, ester-containing organic phase 36 is introduced into vessel 50 in which the alcohol esters are reacted with one or more substances 52 to recover product alcohol 54. Product alcohol 54 can be recovered using any method known in the art for obtaining an alcohol from an alcohol ester. For example, in some embodiments, the product alcohol can be recovered from the alcohol ester by hydrolysis with base followed by acidification. In other embodiments the product alcohol esters can be hydrolyzed by water in the presence of a hydrolysis catalyst as substance 52. For example, in some embodiments, hydrolysis of the product alcohol esters to alcohol and carboxylic acid 28 (e.g., fatty acid when carboxylic acid 28 is a fatty acid) can be achieved using a lipase, a water soluble acid, an inorganic acid, an organic acid, or a solid acid catalyst as substance 52. For example, sulfuric acid can be used as an inorganic acid catalyst for alcohol ester hydrolysis. In some embodiments, the product alcohol can be recovered from the alcohol ester by transesterification with glycerol to make acylglycerols. Some suitable hydrolysis catalysts are lipase enzymes; esterase enzymes; inorganic acids such as sulfuric acid, hydrochloric acid, phosphoric acid, or strong inorganic acids; organic acids such as toluenesulfonic acid, naphthalenesulfonic acid, or strong organic acids; solid acid catalysts such as Amberlyst® sulfonated polystyrene resins, or zeolites; bases such as potassium hydroxide, sodium hydroxide, calcium hydroxide, or strong bases. Additional suitable hydrolysis catalysts include calcium stearate, calcium oleate, zinc stearate, zinc oleate (which may be formed in situ by adding calcium oxide, calcium hydroxide, zinc oxide, or zinc hydroxide, respectively, to the reaction) as well as other water insoluble fatty acid salts and multi-valent metal oxides. In some embodiments, hydrolysis of the alcohol esters can be achieved using steam as substance 52, by increasing temperature, and/or by application of pressure.

In some embodiments, hydrolysis of the alcohol esters can be carried out in a column, for example, a reactive distillation column. Examples 45 to 54 and 56 to 58 demonstrate several methods to recover the product alcohol from an alcohol ester. In some embodiments, by-products 56 are obtained from recovering product alcohol 54. By-products 56 do not include carboxylic acid 28 that can be recovered from hydrolysis of the alcohol esters. Example 67 demonstrates the recovery of product alcohol using irreversible base hydrolysis. Suitable bases include, but are not limited to, sodium hydroxide, potassium hydroxide, calcium hydroxide, and sodium carbonate. The base hydrolysis generates the cation salt of the fatty acid, for example, the potassium or sodium salt of the corn oil fatty acid. This process may require neutralization with acid to return the fatty acid to acid form. Suitable acids for this neutralization include, but are not limited to, sulfuric acid, hydrochloric acid, and nitric acid.

In some embodiments, hydrolysis of the alcohol esters of fatty acids present in the ester-containing organic phase 36 into the product alcohol and free fatty acids occurs at a fatty acid to water ratio from about 10:1 to about 1:10 or in other embodiments, at a fatty acid to water ratio from about 100:1 to about 1:100. In some embodiments, the alcohol esters of fatty acids are hydrolyzed with water at a temperature less than about 100° C. In some embodiments, the hydrolysis occurs at a temperature greater than 100° C., greater than 150° C., greater than 200° C., or greater than 250° C.

For example, in some embodiments, the alcohol esters can be transesterified to produce product alcohol 54 and in some embodiments, a second alcohol ester 56, for example, fatty acid alkyl esters, can also be produced as by-product 56. To achieve such transesterification, the alcohol esters can be contacted with catalysts capable of transesterifying the alcohol esters to release butanol. In some embodiments, the alcohol esters can be transesterified using glycerol to produce product alcohol 54 and acyl glycerides as by-product 56. The acyl glycerides produced may comprise mono- and diacylglycerides. Some suitable catalysts for transesterification reactions are, for example, lipase enzymes, alkoxide salts particularly of the second alcohol, alkyl titanates, soluble inorganic acids such as sulfuric acid and phosphoric acid, soluble organic acids such as toluenesulfonic acid and naphthalenesulfonic acid, and solid acids such as Amberlyst® sulfonated polystyrene resins, or zeolites. Suitable lipases for transesterifications or hydrolysis include, but are not limited to, lipases derived from Burkholderia cepacia, Thermomyces lanuginosa, or Candida antarctica. In some embodiments, the lipases are immobilized on a soluble or insoluble support using methods well-known to those skilled in the art (see, e.g., Immobilization of Enzymes and Cells; Gordon F. Bickerstaff, Editor; Humana Press, Totowa, N.J., USA, 1997). The immobilization of enzymes may be performed using a variety of techniques including 1) binding of the enzyme to a porous or non-porous carrier support, via covalent support, physical adsorption, electrostatic binding, or affinity binding; 2) crosslinking with bifunctional or multifunctional reagents; 3) entrapment in gel matrices, polymers, emulsions, or some form of membrane; and 4) a combination of any of these methods. In other embodiments, the lipases may not be immobilized. In some embodiments, the lipases are soluble. Fatty acid alkyl esters 56 can include fatty acid methyl esters, for example. Other fatty acid alkyl esters 56 can include C₂ to C₁₂ linear, branched, and cyclic alcohol esters, for example. Product alcohol 54 can then be separated from the reaction mixture including by-products 56 using any separation means known in the art such as distillation, for example. Other suitable separation mechanisms can include extraction and membrane separation, for example.

In some embodiments, at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 99% of the product alcohol is recovered from the alcohol esters.

ISPR extractant (carboxylic acid) 28 can be separated from the alcohol esters before reaction of the alcohol esters for recovery of product alcohol 54. Alternatively, ISPR extractant 28 can be separated from the product alcohol and any by-products after the reaction of the alcohol esters. The resulting recovered lean extractant 27 can then be recycled back into fermentation vessel 30, usually in combination with fresh make-up extractant 28 (which can be derived from oil 26, if supplied) for further production and/or extraction of alcohol esters. Alternatively, fresh extractant 28 (or oil 26) can be continuously added to the fermentation vessel to replace the extractant removed in biphasic mixture stream 39.

In some embodiments, catalyst 42 can be recovered from biphasic mixture 39 and reused at a step in the fermentation process such as in the fermentation itself or in recovery of the product alcohol.

In some embodiments, one or more additional ISPR extractants 29 (see FIG. 2) can be introduced into fermentation vessel 30 to form a two-phase mixture comprising an aqueous phase and an organic phase. In such embodiments, ISPR extractant 29 can be an exogenous organic extractant such as oleyl alcohol, behenyl alcohol, cetyl alcohol, lauryl alcohol, myristyl alcohol, stearyl alcohol, 1-undecanol, oleic acid, lauric acid, myristic acid, stearic acid, methyl myristate, methyl oleate, undecanal, lauric aldehyde, 20-methylundecanal, and mixtures thereof. However, for the reasons noted above, ISPR extractant 29 is preferably not an alcohol. Rather, ISPR extractant 29 is preferably a carboxylic acid (e.g. free fatty acids). In some embodiments, ISPR extractant 29 is COFA. In some embodiments, ISPR extractant 29 is linseed oil fatty acid, soybean oil fatty acid, jatropha oil fatty acid, or fatty acids derived from palm oil, castor oil, olive oil, coconut oil, peanut oil, or any seed oil. In some embodiments, ISPR extractant 29 can be a fatty acid extractant selected from the group consisting of fatty acids, fatty alcohols, fatty amides, fatty esters (particularly those comprising 1 to 8 carbon atoms in the alcohol portion, e.g., fatty acid methyl esters and lower alcohol esters of fatty acids), fatty acid glycol esters, hydroxylated triglycerides, and mixtures thereof, obtained from chemical conversion of native oil such as biomass lipids as described, for example, in co-pending, commonly owned U.S. Provisional Application Ser. No. 61/368,436, filed on Jul. 28, 2010, herein incorporated by reference. In some embodiments, ISPR extractant 29 is free fatty acids obtained by chemical hydrolysis of biomass lipids. In some embodiments, ISPR extractant 29 can be free fatty acids produced from enzymatic hydrolysis of native oil such as biomass lipids as described, for example, in co-pending, commonly owned U.S. Provisional Application Ser. No. 61/368,444, filed on Jul. 28, 2010, herein incorporated by reference.

In situ product removal can be carried out in a batch mode or a continuous mode in fermentation vessel 30. In a continuous mode of in situ product removal, product is continually removed from the vessel (or reactor). In a batchwise mode of in situ product removal, a volume of organic extractant is added to the fermentation vessel and the extractant is not removed during the process. For in situ product removal, the organic extractant can contact the fermentation medium at the start of the fermentation forming a biphasic fermentation medium. Alternatively, the organic extractant can contact the fermentation medium after the microorganism has achieved a desired amount of growth which can be determined by measuring the optical density of the culture. Further, the organic extractant can contact the fermentation medium at a time at which the product alcohol level in the fermentation medium reaches a preselected level. In the case of butanol production according to some embodiments of the present invention, at a time before the butanol concentration reaches a toxic level, the carboxylic acid extractant can contact the fermentation medium to esterify the butanol with the carboxylic acid to produce butyl esters and in some embodiments, produce a two-phase mixture comprising an aqueous phase and an organic phase comprising the butyl esters. Consequently, the concentration of butanol is reduced in the fermentation vessel and as a result, minimizes the toxic effects of butanol on the microorganism. The ester-containing organic phase can then be removed from the fermentation vessel (and separated from the fermentation broth which constitutes the aqueous phase) after a desired effective titer of the butyl esters is achieved. For example, in some embodiments, the ester-containing organic phase can be separated from the fermentation broth after the effective titer of butyl esters is greater than about 10 g/kg of fermentation broth. In other embodiments, the ester-containing organic phase can be separated from the fermentation medium after the effective titer of butyl esters is greater than about 230 g/kg fermentation broth, greater than about 300 g/kg fermentation broth, greater than about 400 g/kg fermentation broth, greater than about 500 g/kg fermentation broth, or greater than about 600 g/kg fermentation broth. In another embodiment, the ester-containing organic phase can be separated from the fermentation medium after the % conversion of COFA is at least about 10%, at least about 25%, at least about 50%, at least about 75%, or at least about 100%. In some embodiments, the ester-containing organic phase is separated from the aqueous phase after fermentation of the available fermentable sugar in the fermentation vessel is substantially complete.

In the example embodiment depicted in FIG. 1, the alcohol ester is extracted from the fermentation broth in situ, with the separation of the biphasic mixture 39 occurring in a separate vessel 35. In some embodiments, separation of the biphasic mixture can occur in the fermentation vessel, as shown in the example embodiments of later described FIGS. 3 and 4 in which the ester-containing organic phase stream 36 exits directly from fermentation vessel 30. Aqueous phase stream 34 can also exit directly from fermentation vessel 30, be treated for the removal of any remaining alcohol ester or product alcohol, and recycled, or discarded and replaced with fresh fermentation medium. The extraction of the alcohol ester and the product alcohol by the organic extractant can be done with or without the removal of microorganism 32 from the fermentation broth. Microorganism 32 can be removed from the fermentation broth by means known in the art including, but not limited to, filtration or centrifugation. For example, aqueous phase stream 34 can include microorganism 32 such as yeast. Microorganism 32 can be easily separated from the aqueous phase stream, for example, in a centrifuge (not shown). Microorganism 32 can then be recycled to fermentation vessel 30 which over time can increase the production rate of alcohol production, thereby resulting in an increase in the efficiency of the alcohol production.

In some embodiments, the system and processes of FIG. 1 can be modified such that simultaneous saccharification and fermentation in fermentation vessel 30 is replaced with a separate saccharification vessel 60 prior to fermentation vessel 30, as should be apparent to one of skill in the art (see, e.g., the embodiment of FIG. 4).

In still other embodiments, as shown, for example, in the example embodiment of FIG. 2, native oil 26 (instead of being supplied directly to fermentation vessel 30) is supplied to a vessel 40 to which catalyst 42 is also supplied, whereby at least a portion of the acyl glycerides in oil 26 are hydrolyzed to form carboxylic acid 28. A product stream from vessel 40 containing carboxylic acid 28 and catalyst 42 are then introduced into fermentation vessel 30. Carboxylic acid 28 and catalyst 42 contact the product alcohol produced in the fermentation medium whereby alcohol esters of the product alcohol are formed in situ from catalyzed esterification of the carboxylic acid with the product alcohol, in a same manner as described above with reference to FIG. 1. Carboxylic acid 28 can also serve as an ISPR extractant and in some embodiments, sufficient carboxylic acid 28 and/or one or more additional ISPR extractants 29 can be introduced into fermentation vessel 30 to form a two-phase mixture comprising an aqueous phase and an organic phase, with the alcohol ester partitioning into the organic phase. The remaining process operations of the embodiment of FIG. 2 are identical to FIG. 1 and therefore, will not be described in detail again.

In some embodiments of the present invention, as shown, for example, in the embodiment of FIG. 3, catalyst 42 can be added to feedstock slurry 16 comprising oil 26′ derived from the biomass from which feedstock 12 was formed. In the embodiment shown, catalyst 42 is capable of hydrolyzing the glycerides in oil 26′ to free fatty acids 28′. Thus, after introduction of catalyst 42 to feedstock slurry 16, at least a portion of the glycerides in oil 26′ are hydrolyzed, resulting in a feedstock slurry 18 having free fatty acids 28′ and catalyst 42. For example, when feedstock 12 is corn, then oil 26′ is the feedstock's constituent corn oil and the free fatty acids 28′ are corn oil fatty acids (COFA).

Feedstock slurry 18 is introduced to fermentation vessel 30 along with alcohol-producing microorganism 32 to be included in a fermentation medium. In some embodiments, an enzyme 38 such as glucoamylase, can also be introduced into fermentation vessel for simultaneous saccharification of sugars in slurry 18 and fermentation of alcohol inside fermentation vessel 30. The presence of catalyst 42 in fermentation vessel (introduced via slurry 18) catalyzes the esterification of the alcohol with the free fatty acids 28′ (introduced via slurry 18) to form fatty acid alcohol esters in situ, in a same manner as described above with reference to FIG. 1. In some embodiments, for butanol production, butanol-producing microorganism 32 is introduced in fermentation vessel 30 along with feedstock slurry 18. Catalyst 42 in fermentation vessel (introduced via slurry 18) catalyzes the esterification of the butanol with the free fatty acids 28′ (introduced via slurry 18) to form fatty acid butyl esters (FABE) in situ. Free fatty acids 28′ can also serve as an ISPR extractant. For example, when free fatty acids 28′ are COFA, then alcohol esters of COFA are formed in situ, and COFA serves as an ISPR extractant or a portion thereof.

In some embodiments, one or more additional ISPR extractants 29 can be introduced into fermentation vessel 30 for preferentially partitioning the alcohol ester (and any free alcohol) from the aqueous phase. In some embodiments, ISPR extractant 29 can be carboxylic acid 28 described with reference to the embodiments of FIGS. 1 and 2. In some embodiments, ISPR extractant 29 is introduced in fermentation vessel 30 as oil 26 which is then hydrolyzed into fatty acids by catalyst 42 so as to become ISPR extractant 29. In some embodiments, oil 26 is corn oil, whereby ISPR extractant 29 is COFA. In some embodiments, ISPR extractant 29 can be a fatty acid extractant selected from the group consisting of fatty acids, fatty alcohols, fatty amides, fatty esters (particularly those comprising 1 to 8 carbon atoms in the alcohol portion, e.g., fatty acid methyl esters and lower alcohol esters of fatty acids), fatty acid glycol esters, hydroxylated triglycerides, and mixtures thereof, as described above with reference to the embodiments of FIGS. 1 and 2. In still other embodiments, ISPR extractant 29 can be free fatty acids obtained by chemical or enzymatic hydrolysis of biomass lipids. In such embodiments, the biomass lipids for producing extractant 29 can be from a same or different biomass source from which feedstock 12 is obtained. For example, in some embodiments, the biomass lipids for producing extractant 29 can be derived from soya, whereas the biomass source of feedstock 12 is corn. Any possible combination of different biomass sources for extractant 29 versus feedstock 12 can be used, as should be apparent to one of skill in the art. The remaining process operations of the embodiment of FIG. 2 are identical to FIG. 1 and therefore, will not be described in detail again.

As a non-limiting prophetic example, with reference to the embodiment of FIG. 3, an aqueous suspension of ground whole corn (as feedstock 12) which can nominally contain ca. 4 wt % corn oil, can be treated with amylase (as liquefaction enzyme 14) at ca. 85° C. to 120° C. for 30 minutes to 2 hours, and the resulting liquefied mash 16 cooled to between 65° C. and 30° C. and treated with 0.1 ppm to 10 ppm (in some embodiments, 0.5 ppm to 1.0 ppm) of lipase (as catalyst 42) at pH 4.5 to 7.5 (in some embodiments, between pH 5.5 and 6.5) for sufficient time to produce from at least 30% to as high as at least 99% conversion of the available fatty acid content in lipids to free fatty acids. The liquefied and lipase-treated mash 18 can be cooled to ca. 30° C. (e.g., using a heat-exchanger) and loaded to fermentation vessel 30 at ca. 25% to 30 wt % dry corn solids. Saccharification of the liquefied mash 18 during fermentation by the addition of glucoamylase (as saccharification enzyme 38) can result in the production of glucose. The resulting fermentation broth can contain significantly less than the amount of corn oil (e.g., about 1.2 wt % corn oil) that can be present in a broth using a liquefied mash that has not been treated with lipase 42. In particular, the lipase treatment 42 can result in the conversion of corn oil lipids 26′ (triglycerides (TG)) into COFA 28′ (and some diglycerides (DG) or monoglycerides (MG)), decreasing the rate of build-up of lipids 26′ in the COFA ISPR extraction solvent 28′ or 29. The lipase treatment 42 can also result in the conversion of butanol produced during fermentation to butyl esters of COFA, where the butyl esters of COFA have a high partition coefficient for dissolution into the COFA phase 36 during liquid-liquid extraction ISPR. At the end of fermentation, the COFA phase 36 containing butyl esters of COFA can be separated from the fermentation broth (at vessel 30/35), and the butanol 54 can be recovered (at vessel 50) from this organic mixture 36 using one of several methods including, but not limited to, hydrolysis of the ester using, for example, a lipase 52, a solid acid catalyst 52, or steam 52, to produce butanol 54 and COFA 27.

In still other embodiments, as shown, for example, in the embodiment of FIG. 4, the system and processes of FIG. 3 can be modified such that simultaneous saccharification and fermentation (SSF) in fermentation vessel 30 is replaced with a separate saccharification vessel 60 prior to fermentation vessel 30. FIG. 4 is substantially identical to FIG. 3 except for the inclusion of a separate saccharification vessel 60 receiving enzyme 38, with catalyst 42 being introduced to a liquefied, saccharified feedstock stream 62. Feedstock slurry 16 is introduced into saccharification vessel 60 along with enzyme 38 such as glucoamylase, whereby sugars in the form of oligosaccharides in slurry 16 can be broken down into monosaccharides. A liquefied, saccharified feedstock stream 62 exits saccharification vessel 60 to which catalyst 42 is introduced. Feedstock stream 62 includes monosaccharides, and oil 26′ and undissolved solids derived from the feedstock. Oil 26′ is hydrolyzed by the introduction of catalyst 42, resulting in a liquefied, saccharified feedstock slurry 64 having free fatty acids 28′ and catalyst 42.

Alternatively, in some embodiments, catalyst 42 can be added along with saccharification enzyme 38 to simultaneously produce glucose and hydrolyze oil lipids 26′ to free fatty acids 28′, in a like manner as the introduction of catalyst 42 with enzyme 38 to the fermentation vessel 30 for SSF in the embodiment of FIG. 1. The addition of enzyme 38 and catalyst 42 can be stepwise (e.g., catalyst 42, then enzyme 38, or vice versa), or simultaneous. However, in contrast with the embodiment of FIG. 1 in which the addition of catalyst 42 into fermentation vessel 30 during SSF also substantially simultaneously converts the product alcohol to the alcohol esters, alcohol esters are not formed until slurry 64 containing catalyst 42 is introduced to fermentation vessel 30. Alternatively, in some embodiments, slurry 62 can be introduced to fermentation vessel 30, with catalyst 42 being added directly to the fermentation vessel 30.

In the embodiment of FIG. 4, slurry 64 is introduced to fermentation vessel 30 along with alcohol-producing microorganism 32 which metabolizes the monosaccharides to produce product alcohol. The presence of catalyst 42 in fermentation vessel (introduced via slurry 64) catalyzes the esterification of the alcohol with the free fatty acids 28′ (introduced via slurry 62) to form fatty acid alcohol esters in situ, in the same manner as described above with reference to FIG. 1. Free fatty acids 28′ can also serve as an ISPR extractant for preferentially partitioning the alcohol ester (and any free alcohol) from the aqueous phase. In some embodiments, one or more additional ISPR extractants 29 can also be introduced into fermentation vessel 30 as described above with reference to FIG. 3. The remaining process operations of the embodiment of FIG. 4 are identical to FIG. 3 and therefore, will not be described in detail again.

In some embodiments, including any of the earlier described embodiments with respect to FIGS. 1-4, undissolved solids can be removed from feedstock slurry 16 prior to introduction into fermentation vessel 30. For example, as shown in the embodiment of FIG. 5, feedstock slurry 16 is introduced into an inlet of a separator 20 which is configured to discharge the undissolved solids as a solid phase or wet cake 24. For example, in some embodiments, separator 20 can include a filter press, vacuum filtration, mechanical pressure filtration, or a centrifuge (e.g., decanter centrifuge) for separating the undissolved solids from feedstock slurry 16. In some embodiments, any any conventional centrifuge utilized in the industry, including, for example, a decanter bowl centrifuge, tricanter centrifuge, disk stack centrifuge, filtering centrifuge, or decanter centrifuge may be used to separate the undissolved solids. In some embodiments, removal of the undissolved solids from feedstock slurry 16 can be accomplished by filtration, vacuum filtration, beltfilter, pressure filtration, filtration using a screen, screen separation, grates or grating, porous grating, flotation, hydroclone, filter press, screwpress, gravity settler, vortex separator, or any method that may be used to separate solids from liquids. Optionally, in some embodiments, separator 20 can also be configured to remove some or substantially all of oil 26′ present in feedstock slurry 16. In such embodiments, separator 20 can be any suitable separator known in the art for removing oil from an aqueous feedstream including, but not limited to, siphoning, decantation, centrifugation, using a gravity settler, membrane-assisted phase splitting, and the like. The remaining feedstock including sugar and water is discharged as an aqueous stream 22 to fermentation vessel 30.

For example, in some embodiments, separator 20 includes a tricanter centrifuge 20 that agitates or spins feedstock slurry 16 to produce a centrifuge product comprising an aqueous layer containing sugar and water (i.e., stream 22), a solids layer containing the undissolved solids (i.e., wet cake 24), and an oil layer (i.e., oil stream 26′). In such a case, catalyst 42 can be contacted with the removed oil 26′ to produce a stream of free fatty acid 28′ and catalyst 42. The stream of free fatty acid 28′ and catalyst 42 can then be introduced into fermentation vessel 30 to contact with the fermentation medium, whereby catalytic esterification of product alcohol in the fermentation medium into fatty acid alcohol esters can be achieved in situ, in a same manner as described above with reference to FIG. 1.

Free fatty acids 28′ can also serve as an ISPR extractant 28′, and one or more additional ISPR extractants 29 can also be introduced into fermentation vessel 30. Thus, feedstock oil 26′ can be catalytically hydrolyzed to carboxylic acid, thereby decreasing the amount of lipids present in an ISPR extractant while also producing an ISPR extractant. The ester-containing organic phase 36 can be separated from the aqueous phase 34 of the biphasic mixture 39 at vessel 35, and the product alcohol can be recovered from the alcohol esters in vessel 50 (see FIG. 1). The remaining process operations of the embodiment of FIG. 5 are identical to FIG. 3 and therefore, will not be described in detail again.

When wet cake 24 is removed via centrifuge 20, in some embodiments, a portion of the oil from feedstock 12, such as corn oil when the feedstock is corn, remains in wet cake 24. Wet cake 24 can be washed with additional water in the centrifuge once aqueous solution 22 has been discharged from the centrifuge 20. Washing wet cake 24 will recover the sugar (e.g., oligosaccharides) present in the wet cake and the recovered sugar and water can be recycled to the liquefaction vessel 10. After washing, wet cake 24 may be combined with solubles and then dried to form Dried Distillers' Grains with Solubles (DDGS) through any suitable known process. The formation of the DDGS from wet cake 24 formed in centrifuge 20 has several benefits. Since the undissolved solids do not go to the fermentation vessel, the DDGS does not have trapped extractant and/or product alcohol such as butanol, it is not subjected to the conditions of the fermentation vessel, and it does not contact the microorganisms present in the fermentation vessel. All these benefits make it easier to process and sell DDGS, for example, as animal feed. In some embodiments, oil 26′ is not discharged separately from wet cake 24, but rather oil 26′ is included as part of wet cake 24 and is ultimately present in the DDGS. In such instances, the oil can be separated from the DDGS and converted to an ISPR extractant 29 for subsequent use in the same or different alcohol fermentation process. Methods and systems for removing undissolved solids from feedstock slurry 16 via centrifugation are described in detail in co-pending, commonly owned U.S. Provisional Application Ser. No. 61/356,290, filed Jun. 18, 2010, which is incorporated herein in its entirety by reference thereto.

As described above, oil 26′ may be separated from DDGS using any suitable known process including, for example, a solvent extraction process. In one embodiment of the invention, DDGS are loaded into an extraction vessel and washed with a solvent such as hexane to remove oil 26′. Other solvents that may be utilized include, for example, isobutanol, isohexane, ethanol, petroleum distillates such as petroleum ether, or mixtures thereof. After oil 26′ extraction, DDGS may be treated to remove any residual solvent. For example, DDGS may be heated to vaporize any residual solvent using any method known in the art. Following solvent removal, DDGS may be subjected to a drying process to remove any residual water. The processed DDGS may be used as a feed supplement for animals such as poultry, livestock, and domestic pets.

After extraction from DDGS, the resulting oil 26′ and solvent mixture may be collected for separation of oil 26′ from the solvent. In one embodiment, the oil 26′/solvent mixture may be processed by evaporation whereby the solvent is evaporated and may be collected and recycled. The recovered oil may be converted to an ISPR extractant 29 for subsequent use in the same or different alcohol fermentation process.

In addition to the recovery of solids, it may be desired to recover other by-products of the fermentation process. In one embodiment, fatty acid esters (e.g., fatty acid isobutyl esters) may be recovered, for example, to increase the yield of carbohydrate to product alcohol (e.g., butanol). This may be accomplished, for example, by using a solvent to extract fatty acid isobutyl esters from, for example, the by-product formed by combining and mixing several by-product streams and drying the product of the combining and mixing steps. Such a solvent-based extraction system for recovering corn oil triglyceride from DDGS is described in U.S. Patent Application Publication No. 2010/0092603, the teachings of which are incorporated by reference herein.

In one embodiment of solvent extraction of fatty acid esters, solids may be separated from whole stillage (“separated solids”) since that stream would contain the largest portion, by far, of fatty acid esters in uncombined byproduct streams. These separated solids may then be fed into an extractor and washed with solvent. In one embodiment, the separated solids are turned at least once in order to ensure that all sides of the separated solids are washed with solvent. After washing, the resulting mixture of lipid and solvent, known as miscella, is collected for separation of the extracted lipid from the solvent. For example, the resulting mixture of lipid and solvent may be deposited to a separator for further processing. During the extraction process, as the solvent washes over the separated solids, the solvent not only brings lipid into solution, but it collects fine, solid particles. These “fines” are generally undesirable impurities in the miscella and in one embodiment, the miscella may be discharged from the extractor or separator through a device that separates or scrubs the fines from the miscella.

In order to separate the lipid and the solvent contained in the miscella, the miscella may be subjected to a distillation step. In this step, the miscella can, for example, be processed through an evaporator which heats the miscella to a temperature that is high enough to cause vaporization of the solvent, but is not sufficiently high to adversely affect or vaporize the extracted lipid. As the solvent evaporates, it may be collected, for example, in a condenser, and recycled for future use. Separation of the solvent from the miscella results in a stock of crude lipid which may be further processed to separate water, fatty acid esters (e.g., fatty acid isobutyl esters), fatty acids, and triglycerides.

After extraction of the lipids, the solids may be conveyed out of the extractor and subjected to a stripping process that removes residual solvent. Recovery of residual solvent is important to process economics. In one embodiment, the wet solids can be conveyed in a vapor tight environment to preserve and collect solvent that transiently evaporates from the wet solids as it is conveyed into the desolventizer. As the solids enter the desolventizer, they may be heated to vaporize and remove the residual solvent. In order to heat the solids, the desolventizer may include a mechanism for distributing the solids over one or more trays, and the solids may be heated directly, such as through direct contact with heated air or steam, or indirectly, such as by heating the tray carrying the meal. In order to facilitate transfer of the solids from one tray to another, the trays carrying the solids may include openings that allow the solids to pass from one tray to the next. From the desolventizer, the solids may be conveyed to, optionally, a mixer where the solids are mixed with other by-products before being conveyed into a dryer. An example of solids extraction is described in Example 63. In this example, the solids are fed to a desolventizer where the solids are contacted by steam. In one embodiment, the flows of steam and solids in the desolventizer may be countercurrent. The solids may then exit the desolventizer and may be fed to a dryer or optionally a mixer where various by-products may be mixed. Vapor exiting the desolventizer may be condensed and optionally mixed with miscella and then fed to a decanter. The water-rich phase exiting the decanter may be fed to a distillation column where hexane is removed from the water-rich stream. In one embodiment, the hexane-depleted water rich stream exits the bottom of the distillation column and may be recycled back to the fermentation process, for example, it may be used to slurry the ground corn solids. In another embodiment, the overhead and bottom products may be recycled to the fermentation process. For example, the lipid-rich bottoms may be added to the feed of a hydrolyzer. The overheads may be, for example, condensed and fed to a decanter. The hexane rich stream exiting this decanter can optionally be used as part of the solvent feed to the extractor. The water-rich phase exiting this decanter may be fed to the column that strips hexane out of water. As one skilled in the art can appreciate, the methods of the present invention may be modified in a variety of ways to optimize the fermentation process for the production of a product alcohol such as butanol.

In another embodiment of solvent extraction of fatty acid esters, solids may be separated from beer and solvent discharged from fermentation before they are introduced into a preflash column as a heterogeneous mixture. A wet cake of these solids can be formed using a separation device such as a screen filter or a centrifuge. A screened cake of solids can be displacement washed using hydrous isobutanol to remove fatty acid esters that were retained in the wet solids. Alternatively, a centrifuged cake of solids can be re-pulped in hydrous isobutanol and separated again to effect the removal of fatty acid esters that were retained in the wet solids. An example of this embodiment of solids extraction is described in Example 63.

In a further embodiment, by-products (or co-products) may be derived from the mash used in the fermentation process. For example, corn oil may be separated from mash and this corn oil may contain triglycerides, free fatty acids, diglycerides, monoglycerides, and phospholipids (see, e.g., Example 66). The corn oil may optionally be added to other by-products (or co-products) at different rates and thus, for example, creating the ability to vary the amount of triglyceride in the resulting byproduct. In this manner, the fat content of the resulting by-product could be controlled, for example, to yield a lower fat, high protein animal feed that would better suit the needs of dairy cows compared to a high fat product.

In one embodiment, crude corn oil separated from mash may be further processed into edible oil for consumer use, or it could also be used as a component of animal feed because its high triglyceride content would make it an excellent source of metabolizable energy. In another embodiment, it could also be used as feedstock for biodiesel or renewable diesel.

In one embodiment, extractant by-product may be used, all or in part, as a component of an animal feed by-product or it can be used as feedstock for biodiesel or renewable diesel.

In a further embodiment, solids may be separated from mash and may comprise triglycerides and free fatty acids. These solids (or stream) may be used as an animal feed, either recovered as discharge from centrifugation or after drying. The solids (or wet cake) may be particularly suited as feed for ruminants (e.g., dairy cows) because of its high content of available lysine and by-pass or rumen undegradable protein. For example, these solids may be of particular value in a high protein, low fat feed. In another embodiment, these solids may be used as a base, that is, other by-products such as syrup may be added to the solids to form a product that may be used as an animal feed. In another embodiment, different amounts of other by-products may be added to the solids to tailor the properties of the resulting product to meet the needs of a certain animal species.

The composition of solids separated from whole stillage as described in Example 62 may include, for example, crude protein, fatty acid, and fatty acid isobutyl esters. In one embodiment, this composition (or by-product) may be used, wet or dry, as an animal feed where, for example, a high protein (e.g., high lysine), low fat, and high fiber content is desired. In another embodiment, fat may be added to this composition, for example, from another by-product stream if a higher fat, low fiber animal feed is desired. In one embodiment, this higher fat, low fiber animal feed may be used for swine or poultry. In a further embodiment, a non-aqueous composition of Condensed Distillers Solubles (CDS) (see, e.g., Example 66) may include, for example, protein, fatty acids, and fatty acid isobutyl esters as well as other dissolved and suspended solids such as salts and carbohydrates. This CDS composition may be used, for example, as animal feed, either wet or dry, where a high protein, low fat, high mineral salt feed component is desired. In one embodiment, this composition may be used as a component of a dairy cow ration.

In another embodiment, oil from the fermentation process may be recovered by evaporation. This non-aqueous composition may comprise fatty acid isobutyl esters and fatty acids (see, e.g., Example 66) and this composition (or stream) may be fed to a hydrolyser to recover isobutanol and fatty acids. In a further embodiment, this stream may be used as feedstock for biodiesel production.

The various streams generated by the production of an alcohol (e.g., butanol) via a fermentation process may be combined in many ways to generate a number of co-products. For example, if crude corn from mash is used to generate fatty acids to be utilized as extractant and lipid is extracted by evaporators for other purposes, then the remaining streams may be combined and processed to create a co-product composition comprising crude protein, crude fat, triglycerides, fatty acid, and fatty acid isobutyl ester. In one embodiment, this composition may comprise at least about 20-35 wt % crude protein, at least about 1-20 wt % crude fat, at least about 0-5 wt % triglycerides, at least about 4-10 wt % fatty acid, and at least about 2-6 wt % fatty acid isobutyl ester. In one particular embodiment, the co-product composition may comprise about 25 wt % crude protein, about 10 wt % crude fat, about 0.5 wt % triglycerides, about 6 wt % fatty acid, and about 4 wt % fatty acid isobutyl ester.

In another embodiment, the lipid is extracted by evaporators and the fatty acids are used for other purposes and about 50 wt % of the crude corn from mash and the remaining streams are combined and processed, the resulting co-product composition may comprise crude protein, crude fat, triglycerides, fatty acid, and fatty acid isobutyl ester. In one embodiment, this composition may comprise at least about 25-31 wt % crude protein, at least about 6-10 wt % crude fat, at least about 4-8 wt % triglycerides, at least about 0-2 wt % fatty acid, and at least about 1-3 wt % fatty acid isobutyl ester. In one particular embodiment, the co-product composition may comprise about 28 wt % crude protein, about 8 wt % crude fat, about 6 wt % triglycerides, about 0.7 wt % fatty acid, and about 1 wt % fatty acid isobutyl ester.

In another embodiment, the solids separated from whole stillage and 50 wt % of the corn oil extracted from mash are combined and the resulting co-product composition may comprise crude protein, crude fat, triglycerides, fatty acid, fatty acid isobutyl ester, lysine, neutral detergent fiber (NDF), and acid detergent fiber (ADF). In one embodiment, this composition may comprise at least about 26-34 wt % crude protein, at least about 15-25 wt % crude fat, at least about 12-20 wt % triglycerides, at least about 1-2 wt % fatty acid, at least about 2-4 wt % fatty acid isobutyl ester, at least about 1-2 wt % lysine, at least about 11-23 wt % NDF, and at least about 5-11 wt % ADF. In one particular embodiment, the co-product composition may comprise about 29 wt % crude protein, about 21 wt % crude fat, about 16 wt % triglycerides, about 1 wt % fatty acid, about 3 wt % fatty acid isobutyl ester, about 1 wt % lysine, about 17 wt % NDF, and about 8 wt % ADF. The high fat, triglyceride, and lysine content and the lower fiber content of this co-product composition may be desirable as feed for swine and poultry.

As described above, the various streams generated by the production of an alcohol (e.g., butanol) via a fermentation process may be combined in many ways to generate a co-product composition comprising crude protein, crude fat, triglycerides, fatty acid, and fatty acid isobutyl ester. For example, a composition comprising at least about 6% crude fat and at least about 28% crude protein may be utilized as an animal feed product for dairy animals. A composition comprising at least about 6% crude fat and at least about 26% crude protein may be utilized as an animal feed product for feedlot cattle whereas a composition comprising at least about 1% crude fat and at least about 27% crude protein may be utilized as an animal feed product for wintering cattle. A composition comprising at least about 13% crude fat and at least about 27% crude protein may be utilized as an animal feed product for poultry. A composition comprising at least about 18% crude fat and at least about 22% crude protein may be utilized as an animal feed product for monogastric animals. Thus, the various streams may be combined in such a way as to customize a feed product for a specific animal species.

In one embodiment, one or more streams generated by the production of an alcohol (e.g., butanol) via a fermentation process may be combined in many ways to generate a composition comprising at least about 90% COFA which may be used as fuel source such as biodiesel.

As an example of one embodiment of the methods of the invention, milled grain (e.g., corn processed by hammer mill) and one or more enzymes are combined to generate a slurried grain. This slurried grain is cooked, liquified, and optionally flashed with flash vapor resulting in a cooked mash. The cooked mash is then filtered to remove suspended solids, generating a wet cake and a filtrate. The filtration may be accomplished by several methods such as centrifugation, screening, or vacuum filtration and this filtration step may remove at least about 80% to at least about 99% of the suspended solids from the mash.

The wet cake is reslurried with water and refiltered to remove additional starch, generating a washed filter cake. The reslurry process may be repeated a number of times, for example, one to five times. The water used to reslurry the wet cake may be recycled water generated during the fermentation process. The filtrate produced by the reslurry/refiltration process may be returned to the initial mix step to form a slurry with the milled grain. The filtrate may be heated or cooled prior to the mix step.

The washed filter cake may be reslurried with beer at a number of stages during the production process. For example, the washed filter cake may be reslurried with beer after the fermentor, before the preflash column, or at the feedpoint to the distillers grain dryer. The washed filter cake may be dried separately from other by-products or may be used directly as wet cake for generation of DDGS or an animal feed product.

The filtrate produced as a result of the initial mix step may be further processed as described herein. For example, the filtrate may be heated with steam or process to process heat exchange. A saccharification enzyme may be added to the filtrate and the dissolved starch of the filtrate may be partially or completely saccharified. The saccharified filtrate may be cooled by a number of means such as process to process exchange, exchange with cooling water, or exchange with chilled water.

The cooled filtrate may then be added to a fermentor as well as a microorganism that is suitable for alcohol production, for example, a recombinant yeast capable of producing butanol. In addition, ammonia and recycle streams may also be added to the fermentor. This process may include at least one fermentor, at least two fermentors, at least three fermentors, or at least four fermentors. Carbon dioxide generated during the fermentation may be vented to a scrubber in order to reduce air emissions (e.g., butanol air emissions) and to increase product yield.

Solvent may be added to the fermentor via a recycled loop or may be added directly into the fermentor. The solvent may be one or more organic compounds which have the ability to dissolve or react with the alcohol (e.g., butanol) and may have limited solubility in water. The solvent may be taken from the fermentor continually as a single liquid phase or as a two liquid phase material, or the solvent may be withdrawn batchwise as a single or two liquid phase material.

Beer may be degassed. The beer may be heated before degassing, for example, by process to process exchange with hot mash or process to process exchange with preflash column overheads. Vapors may be vented to a condenser and then, to a scrubber. Degassed beer may be heated further, for example, by process to process heat exchange with other streams in the distillation area.

Preheated beer and solvent may enter a preflash column which may be retrofit from a beer column of a conventional dry grind fuel ethanol plant. This column may be operated at sub-atmospheric pressure, driven by water vapor taken from an evaporator train or from the mash cook step. The overheads of the preflash column may be condensed by heat exchange with some combination of cooling water and process to process heat exchange including heat exchange with the preflash column feed. The liquid condensate may be directed to an alcohol/water decanter (e.g., butanol/water decanter).

The preflash column bottoms may be advanced to a solvent decanter. The preflash column bottoms may be substantially stripped of free alcohol (e.g., butanol). The decanter may be a still well, a centrifuge, or a hydroclone. Water is substantially separated from the solvent phase in this decanter, generating a water phase. The water phase including suspended and dissolved solids may be centrifuged to produce a wet cake and thin stillage. The wet cake may be combined with other streams and dried to produce DDGS, it may be dried and sold separate from other streams which produce DDGS, or it may be sold as a wet cake. The water phase may be split to provide a backset which is used in part to reslurry the filter cake described above. The split also provides thin stillage which may be pumped to evaporators for further processing.

The organic phase produced in the solvent decanter may be an ester of an alcohol (e.g., butanol). The solvent may be hydrolyzed to regenerate reactive solvent and to recover additional alcohol (e.g., butanol). Alternatively, the organic phase may be filtered and sold as a product. Hydrolysis may be thermally driven, homogeneously catalyzed, or heterogeneously catalyzed. Hydrolysis may also occur by enzymatic reaction. The heat input to this process may be a fired heater, hot oil, electrical heat input, or high pressure steam. Water added to drive the hydrolysis may be from a recycled water stream, fresh water, or steam.

Cooled hydrolyzed solvent may be pumped into a sub-atmospheric solvent column where it may be substantially stripped of alcohol (e.g., butanol) with steam. This steam may be water vapor from evaporators, it may be steam from the flash step of the mash process, or it may be steam from a boiler (see, e.g., U.S. Patent Application Publication No. 2009/0171129, incorporated herein by reference). A rectifier column from a conventional dry grind ethanol plant may be suitable as a solvent column. The rectifier column may be modified to serve as a solvent column. The bottoms of the solvent column may be cooled, for example, by cooling water or process to process heat exchange. The cooled bottoms may be decanted to remove residual water and this water may be recycled to other steps with the process or recycled to the mash step.

The solvent column overheads may be cooled by exchange with cooling water or by process to process heat exchange, and the condensate may be directed to a vented alcohol/water decanter (e.g., butanol/water decanter) which may be shared with the preflash column overheads. Other mixed water and alcohol (e.g., butanol) streams may be added to this decanter including the scrubber bottoms and condensate from the degas step. The vent which comprises carbon dioxide, may be directed to a water scrubber. The aqueous layer of this decanter may also be fed to the solvent column or may be stripped of alcohol (e.g., butanol) in a small dedicated distillation column. The aqueous layer may be preheated by process to process exchange with the preflash column overheads, solvent column overheads, or solvent column bottoms. This dedicated column may be modified from the side stripper of a conventional dry grind fuel ethanol process.

The organic layer of the alcohol/water decanter (e.g., butanol/water decanter) may be pumped to an alcohol (e.g., butanol) column. This column may be a super-atmospheric column and may be driven by steam condensation within a reboiler. The feed to the column may be heated by process to process heat exchange in order to reduce the energy demand to operate the column. This process to process heat exchanger may include a partial condenser of the preflash column, a partial condenser of a solvent column, the product of the hydrolyzer, water vapor from the evaporators, or the butanol column bottoms. The condensate of the alcohol (e.g., butanol) column vapor may be cooled and may be returned to the alcohol/water decanter (e.g., butanol/water decanter). The alcohol (e.g., butanol) column bottoms may be cooled by process to process heat exchange including exchange with the alcohol (e.g., butanol) column feed and may be further cooled with cooling water, filtered, and are sold as product alcohol (e.g., butanol).

Thin stillage generated from the preflash column bottoms as described above may be directed to a multiple effect evaporator. This evaporator may have two, three, or more stages. The evaporator may have a configuration of four bodies by two effects similar to the conventional design of a fuel ethanol plant, it may have three bodies by three effects, or it may have other configurations. Thin stillage may enter at any of the effects. At least one of the first effect bodies may be heated with vapor from the super-atmospheric alcohol (e.g., butanol) column. The vapor may be taken from the lowest pressure effect to provide heat in the form of water vapor to the sub-atmospheric preflash column and solvent column. Syrup from the evaporators may be added to the distiller's grain dryer.

Carbon dioxide emissions from the fermentor, degasser, alcohol/water decanter (e.g., butanol/water decanter) and other sources may be directed to a water scrubber. The water supplied to the top of this scrubber may be fresh makeup water or may be recycled water. The recycled water may be treated (e.g., biologically digested) to remove volatile organic compounds and may be chilled. Scrubber bottoms may be sent to the alcohol/water decanter (e.g., butanol/water decanter), to the solvent column, or may be used with other recycled water to reslurry the wet cake described above. Condensate from the evaporators may be treated with anaerobic biological digestion or other processes to purify the water before recycling to reslurry the filter cakes.

If corn is used as the source of the milled grain, corn oil may be separated from the process streams at any of several points. For example, a centrifuge may be operated to produce a corn oil stream following filtration of the cooked mash or the preflash column water phase centrifuge may be operated to produce a corn oil stream. Intermediate concentration syrup for final syrup may be centrifuged to produce a corn oil stream.

In another example of an embodiment of the methods of the invention, the material discharged from the fermentor may be processed in a separation system that involves devices such as a centrifuge, settler, hydrocyclone, etc., and combinations thereof to effect the recovery of live yeast in a concentrated form that can be recycled for reuse in a subsequent fermentation batch either directly or after some re-conditioning. This separation system may also produce an organic stream that comprises fatty esters (e.g. isobutyl fatty esters) and an alcohol (e.g., isobutanol) produced from the fermentation and an aqueous stream containing only trace levels of immiscible organics. This aqueous stream may be used either before or after it is stripped of the alcohol (e.g., isobutanol) content to re-pulp and pump the low starch solids that was separated and washed from liquefied mash. This has the advantage of avoiding what might otherwise be a long belt-driven conveying system to transfer these solids from the liquefaction area to the grain drying and syrup blend area. Furthermore, this whole stillage that results after the alcohol (e.g., isobutanol) has been stripped will need to be separated into thin stillage and wet cake fractions either using existing or new separation devices and this thin stillage will form in part the backset that returns to combine with cook water for preparing a new batch of fermentable mash. Another advantage of this embodiment is that any residual dissolved starch that was retained in the moisture of the solids separated from the liquefied mash would in part be captured and recovered through this backset. Alternatively, the yeast contained in the solids stream may be considered nonviable and may be redispersed in the aqueous stream and this combined stream distilled of any alcohol (e.g., butanol) content remaining from fermentation. Non viable organisms may further be separated for use as a nutrient in the propagation process.

In another embodiment, the multi-phase material may leave the bottom of the pre-flash column and may be processed in a separation system as described above. The concentrated solids may be redispersed in the aqueous stream and this combined stream may be used to re-pulp and pump the low starch solids that were separated and washed from liquefied mash.

The process described above as well as other processes described herein may be demonstrated using computational modeling such as Aspen modeling (see, e.g., U.S. Pat. No. 7,666,282). For example, the commercial modeling software Aspen Plus® (Aspen Technology, Inc., Burlington, Mass.) may be use in conjunction with physical property databases such as DIPPR, available from American Institute of Chemical Engineers, Inc. (New York, N.Y.) to develop an Aspen model for an integrated butanol fermentation, purification, and water management process. This process modeling can perform many fundamental engineering calculations, for example, mass and energy balances, vapor/liquid equilibrium, and reaction rate computations. In order to generate an Aspen model, information input may include, for example, experimental data, water content and composition of feedstock, temperature for mash cooking and flashing, saccharification conditions (e.g., enzyme feed, starch conversion, temperature, pressure), fermentation conditions (e.g., microorganism feed, glucose conversion, temperature, pressure), degassing conditions, solvent columns, preflash columns, condensers, evaporators, centrifuges, etc.

The present invention provides systems and methods for producing a fermentative product such as a product alcohol, through fermentation as well as increasing biomass processing productivity and cost effectiveness. In some embodiments, the product alcohol is butanol. A feedstock can be liquefied to create a feedstock slurry, wherein the feedstock slurry includes soluble sugar and undissolved solids. If the feedstock slurry is fed directly to the fermentor, the undissolved solids may interfere with efficient removal and recovery of a product alcohol such as butanol from the fermentor. In particular, when liquid-liquid extraction is utilized to extract butanol from the fermentation broth, the presence of the undissolved particulates may cause system inefficiencies including, but not limited to, decreasing the mass transfer rate of the butanol to the extractant by interfering with the contact between the extractant and the fermentation broth; creating an emulsion in the fermentor and thereby interfering with good phase separation of the extractant and the fermentation broth; reducing the efficiency of recovering and recycling the extractant because at least a portion of the extractant and butanol becomes “trapped” in the solids which are ultimately removed as DDGS; a lower fermentor volume efficiency because there are solids taking up volume in the fermentor and because there is a slower disengagement of the extractant from the fermentation broth; and shortening the life cycle of the extractant by contamination with corn oil. All of these effects result in higher capital and operating costs. In addition, the extractant “trapped” in the DDGS may detract from DDGS value and qualification for sale as animal feed. Thus, in order to avoid and/or minimize these problems, at least a portion of the undissolved particles (or solids) are removed from the feedstock slurry prior to the addition of sugar present in the feedstock slurry to the fermentor. Extraction activity and the efficiency of the butanol production are increased when extraction is performed on a fermentation broth containing an aqueous solution wherein undissolved particles have been removed relative to extraction performed on a fermentation broth containing an aqueous solution wherein undissolved particles have not been removed.

Extractive fermentation without the presence of the undissolved solids can lead to higher mass transfer rate of the product alcohol from the fermentation broth to the extractant, better phase separation of the extractant from the fermentation inside or external to the fermentor, and lower hold up of the extractant as a result of higher extractant droplet rise velocities. Also, for example, the extractant droplets held up in the fermentation broth during fermentation will disengage from the fermentation broth faster and more completely, thereby resulting in less free extractant in the fermentation broth and can decrease the amount of extractant lost in the process. In addition, for example, the microorganism can be recycled and additional equipment in the downstream processing can be eliminated, such as for example, a beer column and/or some or all of the whole stillage centrifuges. Further, for example, the possibility of extractant being lost in the DDGS is removed. Also, for example, the ability to recycle the microorganism can increase the overall rate of product alcohol production, lower the overall titer requirement, and/or lower the aqueous titer requirement, thereby leading to a healthier microorganism and a higher production rate. In addition, for example, it can be possible to eliminate an agitator in the fermentor to reduce capital costs; to increase the fermentor productivity since the volume is used more efficiently because the extractant hold up is minimized and the undissolved solids are not present; and/or to use continuous fermentation or smaller fermentors in a greenfield plant.

Examples of increased extraction efficiency can include, for example, a stabilized partition coefficient, enhanced (e.g., quicker or more complete) phase separation, enhanced liquid-liquid mass transfer coefficient, operation at a lower titer, increased process stream recyclability, increased fermentation volume efficiency, increased feedstock (e.g., corn) load feeding, increased butanol titer tolerance of the microorganism (e.g., a recombinant microorganism), water recycling, reduction in energy, increased recycling of extractant, and/or recycling of the microorganism.

For example, the volume of the fermentor taken up by solids will be decreased. Thus, the effective volume of the fermentor available for the fermentation can be increased. In some embodiments, the volume of the fermentor available for the fermentation is increased by at least about 10%.

For example, there can be a stabilization in partition coefficient. Because the corn oil in the fermentor can be reduced by removing the solids from the feedstock slurry prior to fermentation, the extractant is exposed to less corn oil which combines with the extractant and may lower the partition coefficient if present in sufficient amount. Therefore, reduction of the corn oil introduced into the fermentor results in a more stable partition coefficient of the extractant phase in the fermentor. In some embodiments, the partition coefficient is decreased by less than about 10% over 10 fermentation cycles.

For example, there can be an increase in the extraction efficiency of the butanol with extractant because there will be a higher mass transfer rate (e.g., in the form of a higher mass transfer coefficient) of the product alcohol from the fermentation broth to the extractant, thereby resulting in an increased efficiency of product alcohol production. In some embodiments, the mass transfer coefficient is increased at least 2-fold (see Examples 4 and 5).

In addition, there can be an increase in phase separation between the fermentation broth and the extractant that reduces the likelihood of the formation of an emulsion, thereby resulting in an increased efficiency of product alcohol production. For example, the phase separation can occur more quickly or can be more complete. In some embodiments, a phase separation may occur where previously no appreciable phase separation was observed in 24 hours. In some embodiments, the phase separation occurs at least about 2× as quickly, at least about 5× as quickly, or at least about 10× as quickly as compared to the phase separation where solids have not been removed (see Examples 6 and 7).

Further, there can be an increase in the recovery and recycling of the extractant. The extractant will not be “trapped” in the solids which may ultimately be removed as DDGS, thereby resulting in an increased efficiency of product alcohol production (see Examples 8 and 9). Also, there will be less dilution of the extractant with corn oil, and there may be less degradation of the extractant (see Example 10).

Also, the flow rate of the extractant can be reduced which will lower operating costs, thereby resulting in an increased efficiency of product alcohol production.

Further still, hold up of the extractant will be decreased as a result of extractant droplets rising at a higher velocity, thereby resulting in an increased efficiency of product alcohol production. Reducing the amount of undissolved solids in the fermentor will also result in an increased efficiency of product alcohol production.

In addition, an agitator can be removed from the fermentor because it is no longer needed to suspend the undissolved solids, thereby reducing capital costs and energy, and increasing the efficiency of the product alcohol production.

FIGS. 1-5 provide various non-limiting embodiments of methods and systems involving fermentation processes in which alcohol esters are produced in situ, extracted from the fermentation medium, and reacted to recover product alcohol. FIGS. 1-5 also provide various non-limiting embodiments of methods and systems of using carboxylic acid that can be esterified with product alcohol and can contemporaneously serve as an ISPR extractant. FIGS. 1-5 also provide various non-limiting embodiments of methods and systems of converting lipids in a feedstock to carboxylic acid that can be esterified with product alcohol and can contemporaneously serve as an ISPR extractant.

In some embodiments, including any of the aforementioned embodiments described with reference to FIGS. 1-5, the fermentation broth in fermentation vessel 30 includes at least one recombinant microorganism 32 which is genetically modified (that is, genetically engineered) to produce butanol via a biosynthetic pathway from at least one fermentable carbon source. In particular, recombinant microorganisms can be grown in a fermentation broth which contains suitable carbon substrates. Additional carbon substrates may include, but are not limited to, monosaccharides such as fructose and galactose; oligosaccharides such as lactose maltose, or sucrose; polysaccharides such as starch or cellulose; or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt. Other carbon substrates may include ethanol, lactate, succinate, or glycerol.

Additionally, the carbon substrate may also be one-carbon substrates such as carbon dioxide or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates, methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine, and a variety of amino acids for metabolic activity. For example, methylotrophic yeasts are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion, et al., Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32, Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter et al., Arch. Microbiol. 153:485-489, 1990). Hence, it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.

Although it is contemplated that all of the above mentioned carbon substrates and mixtures thereof are suitable, in some embodiments, the carbon substrates are glucose, fructose, and sucrose, or mixtures of these with C5 sugars such as xylose and/or arabinose for yeasts cells modified to use C5 sugars. Sucrose may be derived from renewable sugar sources such as sugar cane, sugar beets, cassava, sweet sorghum, and mixtures thereof. Glucose and dextrose may be derived from renewable grain sources through saccharification of starch-based feedstocks including grains such as corn, wheat, rye, barley, oats, and mixtures thereof. In addition, fermentable sugars may be derived from renewable cellulosic or lignocellulosic biomass through processes of pretreatment and saccharification, as described, for example, U.S. Patent Application Publication No. 2007/0031918 A1, which is herein incorporated by reference. In addition to an appropriate carbon source (from aqueous stream 22), fermentation broth must contain suitable minerals, salts, cofactors, buffers, and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of an enzymatic pathway for production of a product alcohol.

From the above discussion and the Examples, one skilled in the art can ascertain essential characteristics of the present invention and can make various changes and modifications of the invention to adapt to various uses and conditions without departing from the present invention. For example, in some embodiments, alcohol esterification and extraction according to the present invention can be employed pre-fermentation, that is, during seed culturing of microorganisms 32 prior to fermentation in fermentation vessel 30. Typically, microorganisms 32 such as yeast can be grown from a seed culture to a desired cell concentration before being harvested and inoculated into fermentation vessel 30, as known in the art.

The carbon source feedstock is an important cost factor in microorganism production such as yeast production and consequently, the biomass yield on sugar is an important optimization criterion. Because the ATP yield from the alcoholic fermentation is much lower than that from the respiratory sugar dissimilation, occurrence of alcoholic fermentation negatively affects the biomass yield and is sought to be avoided during the yeast production (i.e., seed culturing). Nonetheless, the culturing of microorganisms in a seed culture medium can produce an amount of fermentation product including alcohol. For example, in S. cerevisiae yeast, the alcoholic fermentation and respiration occur simultaneously whenever the specific growth rate (μ) and/or the sugar concentration in aerobic cultures exceed a critical value (see, e.g., van Hoek, et al., Biotechnol. Bioeng. 68:517-523, 2000). In order to achieve high biomass yield, the yeast growth is typically controlled, for example, by respiratory conditions using fed-batch fermentation technology for seed culturing. For example, sugar is fed at a low rate resulting in a low sugar concentration in the culture and a low rate of sugar uptake such that sugar metabolism can be substantially respiratory. Under these conditions, high biomass yields can be obtained and accumulation of toxic products can be minimized. In practice, in large scale fed-batch industrial processes, the cells can be exposed to concentration gradients due to an inefficient mixing (see, e.g., Enfors, et al., J. Biotechnol. 85:175-185, 2001). Production and reassimilation of fermentation by-products can be one of the reasons for reduction of biomass yield per glucose in large scale bioreactors compared to laboratory scale.

However, at these conditions, when culturing butanol-producing yeast, for example, the fermentation product including butanol cannot be reassimilated and may accumulate in the culture medium which can be toxic to the microorganisms at high concentration. If product accumulation exceeds critical cell growth inhibitory concentrations (e.g., cell growth is lower than the growth that may be limited by the feed), then a loss of fed-batch control may occur. According to the present invention, using alcohol esterification and extraction to remove butanol from the culture medium can allow the fed-batch fermentation to proceed despite the problems with inefficient mixing and butanol toxicity.

Thus, according to some embodiments, the seed culture medium can be contacted with catalyst 42 and carboxylic acid 28 leading to the production of alcohol esters by esterification of the product alcohol and ultimately, an improved biomass yield per glucose in large scale bioreactors. Furthermore, the concentration of product alcohol in the culture medium can be controlled by alcohol esterification and thus, minimizing or avoiding the deleterious effects of the product alcohol on the microorganisms. In some embodiments, alcohol esters can be extracted from the seed culture medium and the alcohol recovered from the alcohol esters in the same manner as described above with respect to extraction of alcohol esters from fermentation vessel 30 and recovery of product alcohol 54. In some embodiments, alcohol esterification according to the present invention can be employed to esterify the product alcohol in both the seed culture medium and the fermentation medium. In such embodiments, a higher yield of product alcohol can be achieved for the fermentation process as a whole by recovering not only alcohol esters (and free product alcohol) from the fermentation medium, but also recovering alcohol esters produced during the seed culturing (e.g., recovering alcohol esters and/or product alcohol from a propagation tank). In some embodiments, alcohol esterification according to the present invention can be employed pre-fermentation for removal of alcohol from the seed culture medium, while conventional ISPR of product alcohol can be employed for removal of product alcohol during fermentation in fermentation vessel 30.

Thus, it should be apparent that alcohol esterification and extraction according to the present invention can be employed at various stages in an alcohol fermentation process without departing from the present invention.

The alcohol products produced by the methods of the present invention have a number of applications, for example, as reagents, solvents, and fuel. Butanol produced by the claimed methods may be used directly as a fuel (e.g., biofuel), a fuel additive, an alcohol used for the production of esters that can be used as diesel or biodiesel fuel, a feedstock chemical in the plastics industry, an ingredient in formulated products such as cosmetics, and a chemical intermediate. Butanol may also be used as a solvent for paints, coatings, varnishes, resins, gums, dyes, fats, waxes, resins, shellac, rubbers, and alkaloids. Thus, the present invention provides alternative methods to produce alcohols including butanol, which can support the high demand for these industrial chemicals. While not wishing to be bound by theory, it is believed that the processes described herein are useful in conjunction with any alcohol producing microorganism, particularly recombinant microorganisms which produce alcohol at titers above their tolerance levels.

Recombinant Microorganisms and Butanol Biosynthetic Pathways

Alcohol-producing microorganisms are known in the art. For example, fermentative oxidation of methane by methanotrophic bacteria (e.g., Methyiosinus trichosporiurri) produces methanol, and contacting methanol (a C₁ alkyl alcohol) with a carboxylic acid and a catalyst capable of esterifying the carboxylic acid with methanol forms a methanol ester of the carboxylic acid. The yeast strain CEN.PK113-7D (CBS 8340, the Centraal Buro voor Schimmelculture; van Dijken, et al., Enzyme Microb. Techno. 26:706-714, 2000) can produce ethanol, and contacting ethanol with a carboxylic acid and a catalyst capable of esterifying the carboxylic acid with the ethanol forms ethyl ester (see, e.g., Example 36).

Recombinant microorganisms which produce alcohol are also known in the art (e.g., Ohta, et al., Appl. Environ. Microbiol. 57:893-900, 1991; Underwood, et al., Appl. Environ. Microbiol. 68:1071-1081, 2002; Shen and Liao, Metab. Eng. 10:312-320, 2008; Hahnai, et al., Appl. Environ. Microbiol. 73:7814-7818, 2007; U.S. Pat. No. 5,514,583; U.S. Pat. No. 5,712,133; PCT Application Publication No. WO 1995/028476; Feldmann, et al., Appl. Microbiol. Biotechnol. 38: 354-361, 1992; Zhang, et al., Science 267:240-243, 1995; U.S. Patent Application Publication No. 2007/0031918 A1; U.S. Pat. No. 7,223,575; U.S. Pat. No. 7,741,119; U.S. Patent Application Publication No. 2009/0203099 A1; U.S. Patent Application Publication No. 2009/0246846 A1; and PCT Application Publication No. WO 2010/075241, which are herein incorporated by reference).

Suitable recombinant microorganisms capable of producing butanol are known in the art, and certain suitable microorganisms capable of producing butanol are described herein. Recombinant microorganisms to produce butanol via a biosynthetic pathway can include a member of the genera Clostridium, Zymomonas, Escherichia, Salmonella, Serratia, Erwinia, Klebsiella, Shigella, Rhodococcus, Pseudomonas, Bacillus, Lactobacillus, Enterococcus, Alcaligenes, Klebsiella, Paenibacillus, Arthrobacter, Corynebacterium, Brevibacterium, Schizosaccharomyces, Kluyveromyces, Yarrowia, Pichia, Candida, Hansenula, Issatchenkia, or Saccharomyces. In one embodiment, recombinant microorganisms can be selected from the group consisting of Escherichia coli, Lactobacillus plantarum, Kluyveromyces lactis, Kluyveromyces marxianus, and Saccharomyces cerevisiae. In one embodiment, the recombinant microorganism is yeast. In one embodiment, the recombinant microorganism is crabtree-positive yeast selected from Saccharomyces, Zygosaccharomyces, Schizosaccharomyces, Dekkera, Torulopsis, Brettanomyces, and some species of Candida. Species of crabtree-positive yeast include, but are not limited to, Saccharomyces cerevisiae, Saccharomyces kluyveri, Schizosaccharomyces pombe, Saccharomyces bayanus, Saccharomyces mikitae, Saccharomyces paradoxus, Zygosaccharomyces rouxii, and Candida glabrata.

In some embodiments, the host cell is Saccharomyces cerevisiae. S. cerevisiae yeast are known in the art and are available from a variety of sources including, but not limited to, American Type Culture Collection (Rockville, Md.), Centraalbureau voor Schimmelcultures (CBS) Fungal Biodiversity Centre, LeSaffre, Gert Strand AB, Ferm Solutions, North American Bioproducts, Martrex, and Lallemand. S. cerevisiae include, but are not limited to, BY4741, CEN.PK 113-7D, Ethanol Red® yeast, Ferm Pro™ yeast, Bio-Ferm® XR yeast, Gert Strand Prestige Batch Turbo alcohol yeast, Gert Strand Pot Distillers yeast, Gert Strand Distillers Turbo yeast, FerMax™ Green yeast, FerMax™ Gold yeast, Thermosacc® yeast, BG-1, PE-2, CAT-1, CBS7959, CBS7960, and CBS7961.

The production of butanol utilizing fermentation with a microorganism, as well as microorganisms which produce butanol, is disclosed, for example, in U.S. Patent Application Publication No. 2009/0305370, herein incorporated by reference. In some embodiments, microorganisms comprise a butanol biosynthetic pathway. In some embodiments, at least one, at least two, at least three, or at least four polypeptides catalyzing substrate to product conversions of a pathway are encoded by heterologous polynucleotides in the microorganism. In some embodiments, all polypeptides catalyzing substrate to product conversions of a pathway are encoded by heterologous polynucleotides in the microorganism. In some embodiments, the microorganism comprises a reduction or elimination of pyruvate decarboxylase activity. Microorganisms substantially free of pyruvate decarboxylase activity are described in US Application Publication No. 2009/0305363, herein incorporated by reference. Microorganisms substantially free of an enzyme having NAD-dependent glycerol-3-phosphate dehydrogenase activity such as GPD2 are also described therein.

Suitable biosynthetic pathways for production of butanol are known in the art, and certain suitable pathways are described herein. In some embodiments, the butanol biosynthetic pathway comprises at least one gene that is heterologous to the host cell. In some embodiments, the butanol biosynthetic pathway comprises more than one gene that is heterologous to the host cell. In some embodiments, the butanol biosynthetic pathway comprises heterologous genes encoding polypeptides corresponding to every step of a biosynthetic pathway.

Certain suitable proteins having the ability to catalyze indicated substrate to product conversions are described herein and other suitable proteins are provided in the art. For example, U.S. Patent Application Publication Nos. 2008/0261230, 2009/0163376, and 2010/0197519, incorporated herein by reference, describe acetohydroxy acid isomeroreductases; U.S. Patent Application Publication No. 2010/0081154, incorporated by reference, describes dihydroxyacid dehydratases; an alcohol dehydrogenase is described in U.S. Patent Application Publication No. 2009/0269823, incorporated herein by reference.

It is well understood by one skilled in the art that many levels of sequence identity are useful in identifying polypeptides from other species, wherein such polypeptides have the same or similar function or activity and are suitable for use in the recombinant microorganisms described herein. Useful examples of percent identities include, but are not limited to, 75%, 80%, 85%, 90%, or 95%, or any integer percentage from 75% to 100% may be useful in describing the present invention such as 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%.

1-Butanol Biosynthetic Pathway

A biosynthetic pathway for the production of 1-butanol as well as suitable polypeptides and polynucleotides encoding such polypeptides that may be used is described by Donaldson, et al., in U.S. Patent Application Publication No. 2008/0182308 A1, incorporated herein by reference. This biosynthetic pathway comprises the following substrate to product conversions:

a) acetyl-CoA to acetoacetyl-CoA, which may be catalyzed, for example, by acetyl-CoA acetyltransferase;

b) acetoacetyl-CoA to 3-hydroxybutyryl-CoA, which may be catalyzed, for example, by 3-hydroxybutyryl-CoA dehydrogenase;

c) 3-hydroxybutyryl-CoA to crotonyl-CoA, which may be catalyzed, for example, by crotonase;

d) crotonyl-CoA to butyryl-CoA, which may be catalyzed, for example, by butyryl-CoA dehydrogenase;

e) butyryl-CoA to butyraldehyde, which may be catalyzed, for example, by butyraldehyde dehydrogenase; and

f) butyraldehyde to 1-butanol, which may be catalyzed, for example, by 1-butanol dehydrogenase.

In some embodiments, the 1-butanol biosynthetic pathway comprises at least one gene, at least two genes, at least three genes, at least four genes, or at least five genes that is/are heterologous to the yeast cell. In some embodiments, the recombinant host cell comprises a heterologous gene for each substrate to product conversion of a 1-butanol biosynthetic pathway.

2-Butanol Biosynthetic Pathway

Biosynthetic pathways for the production of 2-butanol as well as suitable polypeptides and polynucleotides encoding such polypeptides that may be used are described by Donaldson, et al., in U.S. Patent Application Publication Nos. 2007/0259410 A1 and 2007/0292927A1, and in PCT Application Publication No. WO 2007/130521, all of which are incorporated herein by reference. One 2-butanol biosynthetic pathway comprises the following substrate to product conversions:

a) pyruvate to alpha-acetolactate, which may be catalyzed, for example, by acetolactate synthase;

b) alpha-acetolactate to acetoin, which may be catalyzed, for example, by acetolactate decarboxylase;

c) acetoin to 2,3-butanediol, which may be catalyzed, for example, by butanediol dehydrogenase;

d) 2,3-butanediol to 2-butanone, which may be catalyzed, for example, by butanediol dehydratase; and

e) 2-butanone to 2-butanol, which may be catalyzed, for example, by 2-butanol dehydrogenase.

In some embodiments, the 2-butanol biosynthetic pathway comprises at least one gene, at least two genes, at least three genes, or at least four genes that is/are heterologous to the yeast cell. In some embodiments, the recombinant host cell comprises a heterologous gene for each substrate to product conversion of a 2-butanol biosynthetic pathway.

Isobutanol Biosynthetic Pathway

Biosynthetic pathways for the production of isobutanol as well as suitable polypeptides and polynucleotides encoding such polypeptides that may be used are described in U.S. Patent Application Publication No. 2007/0092957 A1 and PCT Application Publication No. WO 2007/050671, incorporated herein by reference. One isobutanol biosynthetic pathway comprises the following substrate to product conversions:

a) pyruvate to acetolactate, which may be catalyzed, for example, by acetolactate synthase;

b) acetolactate to 2,3-dihydroxyisovalerate, which may be catalyzed, for example, by acetohydroxy acid reductoisomerase;

c) 2,3-dihydroxyisovalerate to α-ketoisovalerate, which may be catalyzed, for example, by acetohydroxy acid dehydratase;

d) α-ketoisovalerate to isobutyraldehyde, which may be catalyzed, for example, by a branched-chain keto acid decarboxylase; and

e) isobutyraldehyde to isobutanol, which may be catalyzed, for example, by a branched-chain alcohol dehydrogenase.

Suitable polypeptide sequences that encode enzymes which catalyze the substrate to product conversions of the isobutanol biosynthetic pathway as well as E.G. numbers corresponding to suitable enzymes for the indicated pathway steps include, but are not limited to, those in Tables AA and BB. Suitable enzymes associated with the given E.G. numbers will be readily available to those of skill in the art, for example, through the BRENDA database (http://www.brenda-enzymes.org/).

TABLE AA Example polypeptides SEQ ID Pathway step Enzyme NO: a) pyruvate to acetolactate Bacillus subtilis alsS (acetolactate 144 synthase, “ALS”) b) acetolactate to 2,3- Lactococcus lactis ilvC (ketol-acid 145 dihydroxyisovalerate reductoisomerase, “KARI”) c) 2,3-dihydroxyisovalerate Streptococcus mutans ilvD 146 to α-ketoisovalerate (dihydroxyacid dehydratase, “DHAD”) d) α-ketoisovalerate to Lactococcus lactis kivD 147 isobutyraldehyde (branched-chain α-keto acid decarboxylase), codon optimized e) isobutyraldehyde to horse liver alcohol dehydrogenase 148 isobutanol (“ADH”) e) isobutyraldehyde to Achromobacter xylosoxidans sadB 149 isobutanol

TABLE BB E.C. numbers Pathway step E.C. Number: a) pyruvate to acetolactate 2.2.1.6 b) acetolactate to 2,3-dihydroxyisovalerate 1.1.1.86 c) 2,3-dihydroxyisovalerate to 4.2.1.9 α-ketoisovalerate d) α-ketoisovalerate to isobutyraldehyde 4.1.1.72 or 4.1.1.1 e) isobutyraldehyde to isobutanol 1.1.1.265, 1.1.1.1 or 1.1.1.2

Provided herein are recombinant microorganisms comprising an isobutanol biosynthetic pathway comprising steps a)-e) (above) wherein at least one of the enzymes selected from the group of the enzyme catalyzing step c) and the enzyme catalyzing step e) is encoded by a heterologous polynucleotide integrated into the chromosome of the microorganism. In some embodiments, both an enzyme catalyzing step c) is encoded by a heterologous polynucleotide integrated into the chromosome of the microorganism, and enzyme catalyzing step e) is encoded by a heterologous polynucleotide integrated into the chromosome of the microorganism.

Provided herein are polynucleotides suitable for recombinant microorganisms comprising a butanol biosynthetic pathway such as an isobutanol biosynthetic pathway. Such polynucleotides include the coding region of the alsS gene from Bacillus subtilis (nt position 457-2172 of SEQ ID NO: 1) and the ilvC gene from Lactococcus lactis (nt 3634-4656 of SEQ ID NO: 1) as well as plasmids comprising either or both. Also suitable is a chimeric gene having the coding region of the alsS gene from Bacillus subtilis (nt position 457-2172 of SEQ ID NO: 1) expressed from the yeast CUP1 promoter (nt 2-449 of SEQ ID NO: 1) and followed by the CYC1 terminator (nt 2181-2430 of SEQ ID NO: 1) for expression of ALS, and a chimeric gene having the coding region of the ilvC gene from Lactococcus lactis (nt 3634-4656 of SEQ ID NO: 1) expressed from the yeast ILV5 promoter (2433-3626 of SEQ ID NO: 1) and followed by the ILV5 terminator (nt 4682-5304 of SEQ ID NO: 1) for expression of KARI, as well as plasmids comprising either or both chimeric genes.

Suitable polynucleotides include the coding region of the ilvD gene from Streptococcus mutans (nt position 3313-4849 of SEQ ID NO: 2), the coding region of codon optimized horse liver alcohol dehydrogenase (nt 6286-7413 of SEQ ID NO: 2), the coding region of the codon-optimized kivD gene from Lactococcus lactis (nt 9249-10895 of SEQ ID NO: 2) as well as plasmids comprising any or all or any combination thereof. Also suitable is a chimeric gene having the coding region of the ilvD gene from Streptococcus mutans (nt position 3313-4849 of SEQ ID NO: 2) expressed from the S. cerevisiae FBA1 promoter (nt 2109-3105 of SEQ ID NO: 2) followed by the FBA1 terminator (nt 4858-5857 of SEQ ID NO: 2) for expression of DHAD; a chimeric gene having the coding region of codon optimized horse liver alcohol dehydrogenase (nt 6286-7413 of SEQ ID NO: 2) expressed from the S. cerevisiae GPM1 promoter (nt 7425-8181 of SEQ ID NO: 2) followed by the ADH1 terminator (nt 5962-6277 of SEQ ID NO: 2) for expression of ADH; and a chimeric gene having the coding region of the codon-optimized kivD gene from Lactococcus lactis (nt 9249-10895 of SEQ ID NO: 2) expressed from the TDH3 promoter (nt 10896-11918 of SEQ ID NO: 2) followed by the TDH3 terminator (nt 8237-9235 of SEQ ID NO: 2) for expression of KivD as well as plasmids containing any, all, or any combination of such chimeric genes. In addition, suitable polynucleotides include those having at least about 75% identity to the coding regions and chimeric genes specified, as well as plasmids comprising such polynucleotides.

In some embodiments, the isobutanol biosynthetic pathway comprises at least one gene, at least two genes, at least three genes, or at least four genes that is/are heterologous to the yeast cell. In some embodiments, the recombinant host cell comprises a heterologous gene for each substrate to product conversion of an isobutanol biosynthetic pathway.

Suitable strains include those described in certain applications cited and incorporated by reference herein as well as in U.S. Provisional Application Ser. No. 61/380,563, filed on Sep. 7, 2010. Construction of certain suitable strains including those used in the Examples, is provided herein.

Construction of Saccharomyces cerevisiae strain BP1083 (“NGC1-070”; PNY1504)

The strain BP1064 was derived from CEN.PK 113-7D (CBS 8340; Centraalbureau voor Schimmelcultures (CBS) Fungal Biodiversity Centre, Netherlands) and contains deletions of the following genes: URA3, HIS3, PDC1, PDC5, PDC6, and GPD2. BP1064 was transformed with plasmids pYZ090 (SEQ ID NO: 1, described in U.S. Provisional Application Ser. No. 61/246,844) and pLH468 (SEQ ID NO: 2) to create strain NGCI-070 (BP1083, PNY1504).

Deletions, which completely removed the entire coding sequence, were created by homologous recombination with PCR fragments containing regions of homology upstream and downstream of the target gene and either a G418 resistance marker or URA3 gene for selection of transformants. The G418 resistance marker, flanked by loxP sites, was removed using Cre recombinase. The URA3 gene was removed by homologous recombination to create a scarless deletion or if flanked by loxP sites, was removed using Cre recombinase.

The scarless deletion procedure was adapted from Akada, et al., (Yeast 23:399-405, 2006). In general, the PCR cassette for each scarless deletion was made by combining four fragments, A-B-U-C, by overlapping PCR. The PCR cassette contained a selectable/counter-selectable marker, URA3 (Fragment U), consisting of the native CEN.PK 113-7D URA3 gene, along with the promoter (250 bp upstream of the URA3 gene) and terminator (150 bp downstream of the URA3 gene). Fragments A and C, each 500 bp long, corresponded to the 500 bp immediately upstream of the target gene (Fragment A) and the 3′ 500 bp of the target gene (Fragment C). Fragments A and C were used for integration of the cassette into the chromosome by homologous recombination. Fragment B (500 bp long) corresponded to the 500 bp immediately downstream of the target gene and was used for excision of the URA3 marker and Fragment C from the chromosome by homologous recombination, as a direct repeat of the sequence corresponding to Fragment B was created upon integration of the cassette into the chromosome. Using the PCR product ABUC cassette, the URA3 marker was first integrated into and then excised from the chromosome by homologous recombination. The initial integration deleted the gene, excluding the 3′ 500 bp. Upon excision, the 3′ 500 bp region of the gene was also deleted. For integration of genes using this method, the gene to be integrated was included in the PCR cassette between fragments A and B.

URA3 Deletion

To delete the endogenous URA3 coding region, a ura3::loxP-kanMX-IoxP cassette was PCR-amplified from pLA54 template DNA (SEQ ID NO: 3). pLA54 contains the K. lactis TEF1 promoter and kanMX marker, and is flanked by loxP sites to allow recombination with Cre recombinase and removal of the marker. PCR was done using Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers BK505 and BK506 (SEQ ID NOs: 4 and 5). The URA3 portion of each primer was derived from the 5′ region upstream of the URA3 promoter and 3′ region downstream of the coding region such that integration of the loxP-kanMX-IoxP marker resulted in replacement of the URA3 coding region. The PCR product was transformed into CEN.PK 113-7D using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants were selected on YPD containing G418 (100 μg/mL) at 30° C. Transformants were screened to verify correct integration by PCR using primers LA468 and LA492 (SEQ ID NOs: 6 and 7) and designated CEN.PK 113-7D Δura3::kanMX.

HIS3 Deletion

The four fragments for the PCR cassette for the scarless HIS3 deletion were amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs Inc., Ipswich, Mass.) and CEN.PK 113-7D genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact, kit (Qiagen, Valencia, Calif.). HIS3 Fragment A was amplified with primer oBP452 (SEQ ID NO: 14) and primer oBP453 (SEQ ID NO: 15) containing a 5′ tail with homology to the 5′ end of HIS3 Fragment B. HIS3 Fragment B was amplified with primer oBP454 (SEQ ID NO: 16) containing a 5′ tail with homology to the 3′ end of HIS3 Fragment A, and primer oBP455 (SEQ ID NO: 17) containing a 5′ tail with homology to the 5′ end of HIS3 Fragment U. HIS3 Fragment U was amplified with primer oBP456 (SEQ ID NO: 18) containing a 5′ tail with homology to the 3′ end of HIS3 Fragment B, and primer oBP457 (SEQ ID NO: 19) containing a 5′ tail with homology to the 5′ end of HIS3 Fragment C. HIS3 Fragment C was amplified with primer oBP458 (SEQ ID NO: 20) containing a 5′ tail with homology to the 3′ end of HIS3 Fragment U, and primer oBP459 (SEQ ID NO: 21). PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif.). HIS3 Fragment AB was created by overlapping PCR by mixing HIS3 Fragment A and HIS3 Fragment B and amplifying with primers oBP452 (SEQ ID NO: 14) and oBP455 (SEQ ID NO: 17). HIS3 Fragment UC was created by overlapping PCR by mixing HIS3 Fragment U and HIS3 Fragment C and amplifying with primers oBP456 (SEQ ID NO: 18) and oBP459 (SEQ ID NO: 21). The resulting PCR products were purified on an agarose gel followed by a Gel Extraction kit (Qiagen, Valencia, Calif.). The HIS3 ABUC cassette was created by overlapping PCR by mixing HIS3 Fragment AB and HIS3 Fragment UC and amplifying with primers oBP452 (SEQ ID NO: 14) and oBP459 (SEQ ID NO: 21). The PCR product was purified with a PCR Purification kit (Qiagen, Valencia, Calif.).

Competent cells of CEN.PK 113-7D Δura3::kanMX were made and transformed with the HIS3 ABUC PCR cassette using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.). Transformation mixtures were plated on synthetic complete media lacking uracil supplemented with 2% glucose at 30° C. Transformants with a his3 knockout were screened for by PCR with primers oBP460 (SEQ ID NO: 22) and oBP461 (SEQ ID NO: 23) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). A correct transformant was selected as strain CEN.PK 113-7D Δura3::kanMX Δhis3::URA3.

KanMX Marker Removal from the Δura3 Site and URA3 Marker Removal from the Δhis3 Site

The KanMX marker was removed by transforming CEN.PK 113-7D Δura3::kanMX Δhis3::URA3 with pRS423::PGAL1-cre (SEQ ID NO: 66, described in U.S. Provisional Application No. 61/290,639) using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.) and plating on synthetic complete medium lacking histidine and uracil supplemented with 2% glucose at 30° C. Transformants were grown in YP supplemented with 1% galactose at 30° C. for ˜6 hours to induce the Cre recombinase and KanMX marker excision and plated onto YPD (2% glucose) plates at 30° C. for recovery. An isolate was grown overnight in YPD and plated on synthetic complete medium containing 5-fluoro-orotic acid (5-FOA, 0.1%) at 30° C. to select for isolates that lost the URA3 marker. 5-FOA resistant isolates were grown in and plated on YPD for removal of the pRS423::PGAL1-cre plasmid. Isolates were checked for loss of the KanMX marker, URA3 marker, and pRS423::PGAL1-cre plasmid by assaying growth on YPD+G418 plates, synthetic complete medium lacking uracil plates, and synthetic complete medium lacking histidine plates. A correct isolate that was sensitive to G418 and auxotrophic for uracil and histidine was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 and designated as BP857. The deletions and marker removal were confirmed by PCR and sequencing with primers oBP450 (SEQ ID NO: 24) and oBP451 (SEQ ID NO: 25) for Δura3 and primers oBP460 (SEQ ID NO: 22) and oBP461 (SEQ ID NO: 23) for Δhis3 using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.).

PDC6 Deletion

The four fragments for the PCR cassette for the scarless PDC6 deletion were amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs Inc., Ipswich, Mass.) and CEN.PK 113-7D genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). PDC6 Fragment A was amplified with primer oBP440 (SEQ ID NO: 26) and primer oBP441 (SEQ ID NO: 27) containing a 5′ tail with homology to the 5′ end of PDC6 Fragment B. PDC6 Fragment B was amplified with primer oBP442 (SEQ ID NO: 28), containing a 5′ tail with homology to the 3′ end of PDC6 Fragment A, and primer oBP443 (SEQ ID NO: 29) containing a 5′ tail with homology to the 5′ end of PDC6 Fragment U. PDC6 Fragment U was amplified with primer oBP444 (SEQ ID NO: 30) containing a 5′ tail with homology to the 3′ end of PDC6 Fragment B, and primer oBP445 (SEQ ID NO: 31) containing a 5′ tail with homology to the 5′ end of PDC6 Fragment C. PDC6 Fragment C was amplified with primer oBP446 (SEQ ID NO: 32) containing a 5′ tail with homology to the 3′ end of PDC6 Fragment U, and primer oBP447 (SEQ ID NO: 33). PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif.). PDC6 Fragment AB was created by overlapping PCR by mixing PDC6 Fragment A and PDC6 Fragment B and amplifying with primers oBP440 (SEQ ID NO: 26) and oBP443 (SEQ ID NO: 29). PDC6 Fragment UC was created by overlapping PCR by mixing PDC6 Fragment U and PDC6 Fragment C and amplifying with primers oBP444 (SEQ ID NO: 30) and oBP447 (SEQ ID NO: 33). The resulting PCR products were purified on an agarose gel followed by a Gel Extraction kit (Qiagen, Valencia, Calif.). The PDC6 ABUC cassette was created by overlapping PCR by mixing PDC6 Fragment AB and PDC6 Fragment UC and amplifying with primers oBP440 (SEQ ID NO: 26) and oBP447 (SEQ ID NO: 33). The PCR product was purified with a PCR Purification kit (Qiagen, Valencia, Calif.).

Competent cells of CEN.PK 113-7D Δura3::loxP Δhis3 were made and transformed with the PDC6 ABUC PCR cassette using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.). Transformation mixtures were plated on synthetic complete media lacking uracil supplemented with 2% glucose at 30° C. Transformants with a pdc6 knockout were screened for by PCR with primers oBP448 (SEQ ID NO: 34) and oBP449 (SEQ ID NO: 35) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). A correct transformant was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6::URA3.

CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6::URA3 was grown overnight in YPD and plated on synthetic complete medium containing 5-fluoro-orotic acid (0.1%) at 30° C. to select for isolates that lost the URA3 marker. The deletion and marker removal were confirmed by PCR and sequencing with primers oBP448 (SEQ ID NO: 34) and oBP449 (SEQ ID NO: 35) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The absence of the PDC6 gene from the isolate was demonstrated by a negative PCR result using primers specific for the coding sequence of PDC6, oBP554 (SEQ ID NO: 36) and oBP555 (SEQ ID NO: 37). The correct isolate was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 and designated as BP891.

PDC1 Deletion ilvDSm Integration

The PDC1 gene was deleted and replaced with the ilvD coding region from Streptococcus mutans ATCC No. 700610. The A fragment followed by the ilvD coding region from Streptococcus mutans for the PCR cassette for the PDC1 deletion-ilvDSm integration was amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs Inc., Ipswich, Mass.) and NYLA83 genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). NYLA83 is a strain (construction described in U.S. Patent Application Publication No. 2011/0124060, incorporated herein by reference in its entirety) which carries the PDC1 deletion-ilvDSm integration described in U.S. Patent Application Publication No. 2009/0305363, herein incorporated by reference in its entirety). PDC1 Fragment A-ilvDSm (SEQ ID NO: 141) was amplified with primer oBP513 (SEQ ID NO: 38) and primer oBP515 (SEQ ID NO: 39) containing a 5′ tail with homology to the 5′ end of PDC1 Fragment B. The B, U, and C fragments for the PCR cassette for the PDC1 deletion-ilvDSm integration were amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs Inc., Ipswich, Mass.) and CEN.PK 113-7D genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). PDC1 Fragment B was amplified with primer oBP516 (SEQ ID NO: 40) containing a 5′ tail with homology to the 3′ end of PDC1 Fragment A-ilvDSm, and primer oBP517 (SEQ ID NO: 41) containing a 5′ tail with homology to the 5′ end of PDC1 Fragment U. PDC1 Fragment U was amplified with primer oBP518 (SEQ ID NO: 42) containing a 5′ tail with homology to the 3′ end of PDC1 Fragment B, and primer oBP519 (SEQ ID NO: 43) containing a 5′ tail with homology to the 5′ end of PDC1 Fragment C. PDC1 Fragment C was amplified with primer oBP520 (SEQ ID NO: 44), containing a 5′ tail with homology to the 3′ end of PDC1 Fragment U, and primer oBP521 (SEQ ID NO: 45). PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif. PDC1 Fragment A-ilvDSm-B was created by overlapping PCR by mixing PDC1 Fragment A-ilvDSm and PDC1 Fragment B and amplifying with primers oBP513 (SEQ ID NO: 38) and oBP517 (SEQ ID NO: 41). PDC1 Fragment UC was created by overlapping PCR by mixing PDC1 Fragment U and PDC1 Fragment C and amplifying with primers oBP518 (SEQ ID NO: 42) and oBP521 (SEQ ID NO: 45). The resulting PCR products were purified on an agarose gel followed by a Gel Extraction kit (Qiagen, Valencia, Calif.). The PDC1 A-ilvDSm-BUC cassette (SEQ ID NO: 142) was created by overlapping PCR by mixing PDC1 Fragment A-ilvDSm-B and PDC1 Fragment UC and amplifying with primers oBP513 (SEQ ID NO: 38) and oBP521 (SEQ ID NO: 45). The PCR product was purified with a PCR Purification kit (Qiagen, Valencia, Calif.).

Competent cells of CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 were made and transformed with the PDC1 A-ilvDSm-BUC PCR cassette using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.). Transformation mixtures were plated on synthetic complete media lacking uracil supplemented with 2% glucose at 30° C. Transformants with a pdc1 knockout ilvDSm integration were screened for by PCR with primers oBP511 (SEQ ID NO: 46) and oBP512 (SEQ ID NO: 47) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The absence of the PDC1 gene from the isolate was demonstrated by a negative PCR result using primers specific for the coding sequence of PDC1, oBP550 (SEQ ID NO: 48) and oBP551 (SEQ ID NO: 49). A correct transformant was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm-URA3.

CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm-URA3 was grown overnight in YPD and plated on synthetic complete medium containing 5-fluoro-orotic acid (0.1%) at 30° C. to select for isolates that lost the URA3 marker. The deletion of PDC1, integration of ilvDSm, and marker removal were confirmed by PCR and sequencing with primers oBP511 (SEQ ID NO: 46) and oBP512 (SEQ ID NO: 47) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The correct isolate was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm and designated as BP907.

PDC5 Deletion sadB Integration

The PDC5 gene was deleted and replaced with the sadB coding region from Achromobacter xylosoxidans. A segment of the PCR cassette for the PDC5 deletion-sadB integration was first cloned into plasmid pUC19-URA3MCS.

pUC19-URA3MCS is pUC19 based and contains the sequence of the URA3 gene from Saccharomyces cerevisiae situated within a multiple cloning site (MCS). pUC19 contains the pMB1 replicon and a gene coding for beta-lactamase for replication and selection in Escherichia coli. In addition to the coding sequence for URA3, the sequences from upstream and downstream of this gene were included for expression of the URA3 gene in yeast. The vector can be used for cloning purposes and can be used as a yeast integration vector.

The DNA encompassing the URA3 coding region along with 250 bp upstream and 150 bp downstream of the URA3 coding region from Saccharomyces cerevisiae CEN.PK 113-7D genomic DNA was amplified with primers oBP438 (SEQ ID NO: 12) containing BamHI, AscI, PmeI, and FseI restriction sites, and oBP439 (SEQ ID NO: 13) containing XbaI, PacI, and NotI restriction sites, using Phusion® High Fidelity PCR Master Mix (New England BioLabs Inc., Ipswich, Mass.). Genomic DNA was prepared using a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The PCR product and pUC19 (SEQ ID NO: 150) were ligated with T4 DNA ligase after digestion with BamHI and Xbal to create vector pUC19-URA3MCS. The vector was confirmed by PCR and sequencing with primers oBP264 (SEQ ID NO: 10) and oBP265 (SEQ ID NO: 11).

The coding sequence of sadB and PDC5 Fragment B were cloned into pUC19-URA3MCS to create the sadB-BU portion of the PDC5 A-sadB-BUC PCR cassette. The coding sequence of sadB was amplified using pLH468-sadB (SEQ ID NO: 67) as template with primer oBP530 (SEQ ID NO: 50) containing an AscI restriction site, and primer oBP531 (SEQ ID NO: 51) containing a 5′ tail with homology to the 5′ end of PDC5 Fragment B. PDC5 Fragment B was amplified with primer oBP532 (SEQ ID NO: 52) containing a 5′ tail with homology to the 3′ end of sad B, and primer oBP533 (SEQ ID NO: 53) containing a PmeI restriction site. PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif.). sadB-PDC5 Fragment B was created by overlapping PCR by mixing the sadB and PDC5 Fragment B PCR products and amplifying with primers oBP530 (SEQ ID NO: 50) and oBP533 (SEQ ID NO: 53). The resulting PCR product was digested with AscI and PmeI and ligated with T4 DNA ligase into the corresponding sites of pUC19-URA3MCS after digestion with the appropriate enzymes. The resulting plasmid was used as a template for amplification of sadB-Fragment B-Fragment U using primers oBP536 (SEQ ID NO: 54) and oBP546 (SEQ ID NO: 55) containing a 5′ tail with homology to the 5′ end of PDC5 Fragment C. PDC5 Fragment C was amplified with primer oBP547 (SEQ ID NO: 56) containing a 5′ tail with homology to the 3′ end of PDC5 sadB-Fragment B-Fragment U, and primer oBP539 (SEQ ID NO: 57). PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif.). PDC5 sadB-Fragment B-Fragment U-Fragment C was created by overlapping PCR by mixing PDC5 sadB-Fragment B-Fragment U and PDC5 Fragment C and amplifying with primers oBP536 (SEQ ID NO: 54) and oBP539 (SEQ ID NO: 57). The resulting PCR product was purified on an agarose gel followed by a Gel Extraction kit (Qiagen, Valencia, Calif.). The PDC5 A-sadB-BUC cassette (SEQ ID NO: 143) was created by amplifying PDC5 sadB-Fragment B-Fragment U-Fragment C with primers oBP542 (SEQ ID NO: 58) containing a 5′ tail with homology to the 50 nucleotides immediately upstream of the native PDC5 coding sequence, and oBP539 (SEQ ID NO: 57). The PCR product was purified with a PCR Purification kit (Qiagen, Valencia, Calif.).

Competent cells of CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm were made and transformed with the PDC5 A-sadB-BUC PCR cassette using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.). Transformation mixtures were plated on synthetic complete media lacking uracil supplemented with 1% ethanol (no glucose) at 30° C. Transformants with a pdc5 knockout sadB integration were screened for by PCR with primers oBP540 (SEQ ID NO: 59) and oBP541 (SEQ ID NO: 60) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The absence of the PDC5 gene from the isolate was demonstrated by a negative PCR result using primers specific for the coding sequence of PDC5, oBP552 (SEQ ID NO: 61) and oBP553 (SEQ ID NO: 62). A correct transformant was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm Δpdc5::sadB-URA3.

CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm Δpdc5::sadB-URA3 was grown overnight in YPE (1% ethanol) and plated on synthetic complete medium supplemented with ethanol (no glucose) and containing 5-fluoro-orotic acid (0.1%) at 30° C. to select for isolates that lost the URA3 marker. The deletion of PDC5, integration of sadB, and marker removal were confirmed by PCR with primers oBP540 (SEQ ID NO: 59) and oBP541 (SEQ ID NO: 60) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The correct isolate was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm Δpdc5::sadB and designated as BP913.

GPD2 Deletion

To delete the endogenous GPD2 coding region, a gpd2::loxP-URA3-loxP cassette (SEQ ID NO: 151) was PCR-amplified using loxP-URA3-loxP (SEQ ID NO: 68) as template DNA. loxP-URA3-loxP contains the URA3 marker from (ATCC No. 77107) flanked by loxP recombinase sites. PCR was done using Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers LA512 and LA513 (SEQ ID NOs: 8 and 9). The GPD2 portion of each primer was derived from the 5′ region upstream of the GPD2 coding region and 3′ region downstream of the coding region such that integration of the loxP-URA3-loxP marker resulted in replacement of the GPD2 coding region. The PCR product was transformed into BP913 and transformants were selected on synthetic complete media lacking uracil supplemented with 1% ethanol (no glucose). Transformants were screened to verify correct integration by PCR using primers oBP582 and AA270 (SEQ ID NOs: 63 and 64).

The URA3 marker was recycled by transformation with pRS423::PGAL1-cre (SEQ ID NO: 66) and plating on synthetic complete media lacking histidine supplemented with 1% ethanol at 30° C. Transformants were streaked on synthetic complete medium supplemented with 1% ethanol and containing 5-fluoro-orotic acid (0.1%) and incubated at 30° C. to select for isolates that lost the URA3 marker. 5-FOA resistant isolates were grown in YPE (1% ethanol) for removal of the pRS423::PGAL1-cre plasmid. The deletion and marker removal were confirmed by PCR with primers oBP582 (SEQ ID NO: 63) and oBP591 (SEQ ID NO: 65). The correct isolate was selected as strain CEN.PK 113-7D Δura3::loxP Δhis3 Δpdc6 Δpdc1::ilvDSm Δpdc5::sadB Δgpd2::loxP and designated as PNY1503 (BP1064).

BP1064 was transformed with plasmids pYZ090 (SEQ ID NO: 1) and pLH468 (SEQ ID NO: 2) to create strain NGCI-070 (BP1083; PNY1504).

Construction of Saccharomyces cerevisiae Strain PNY2205

The strain, PNY2205, was derived from PNY1503 (BP1064) which is described above.

Deletions, which generally removed the entire coding sequence, were created by homologous recombination with PCR fragments containing regions of homology upstream and downstream of the target gene and the URA3 gene for selection of transformants. The URA3 gene was removed by homologous recombination to create a scarless deletion. Gene integrations were generated in a similar manner.

The scarless deletion procedure was adapted from Akada et al., (Yeast, 23:399, 2006). In general, the PCR cassette for each scarless deletion was made by combining four fragments, A-B-U-C, by overlapping PCR. In some instances, the individual fragments were first cloned into a plasmid prior to the entire cassette being amplified by PCR for the deletion/integration procedure. The PCR cassette contained a selectable/counter-selectable marker, URA3 (Fragment U), consisting of the native CEN.PK 113-7D URA3 gene, along with the promoter (250 bp upstream of the URA3 gene) and terminator (150 bp downstream of the URA3 gene) regions. Fragments A and C, each generally 500 bp long, corresponded to the 500 bp immediately upstream of the target gene (Fragment A) and the 3′ 500 bp of the target gene (Fragment C). Fragments A and C were used for integration of the cassette into the chromosome by homologous recombination. Fragment B (500 bp long) corresponded to the 500 bp immediately downstream of the target gene and was used for excision of the URA3 marker and Fragment C from the chromosome by homologous recombination, as a direct repeat of the sequence corresponding to Fragment B was created upon integration of the cassette into the chromosome.

Using the PCR product ABUC cassette, the URA3 marker was first integrated into and then excised from the chromosome by homologous recombination. The initial integration deleted the gene, excluding the 3′ 500 bp. Upon excision, the 3′ 500 bp region of the gene was also deleted. For integration of genes using this method, the gene to be integrated was included in the PCR cassette between fragments A and B.

FRA2 Deletion

The FRA2 deletion was designed to delete 250 nucleotides from the 3′ end of the coding sequence, leaving the first 113 nucleotides of the FRA2 coding sequence intact. An in-frame stop codon was present 7 nucleotides downstream of the deletion. The four fragments for the PCR cassette for the scarless FRA2 deletion were amplified using Phusion® High Fidelity PCR Master Mix (New England BioLabs Inc., Ipswich, Mass.) and CEN.PK 113-7D genomic DNA as template, prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). FRA2 Fragment A was amplified with primer oBP594 (SEQ ID NO: 152) and primer oBP595 (SEQ ID NO: 153), containing a 5′ tail with homology to the 5′ end of FRA2 Fragment B. FRA2 Fragment B was amplified with primer oBP596 (SEQ ID NO: 154), containing a 5′ tail with homology to the 3′ end of FRA2 Fragment A, and primer oBP597 (SEQ ID NO: 155), containing a 5′ tail with homology to the 5′ end of FRA2 Fragment U. FRA2 Fragment U was amplified with primer oBP598 (SEQ ID NO: 156), containing a 5′ tail with homology to the 3′ end of FRA2 Fragment B, and primer oBP599 (SEQ ID NO: 157), containing a 5′ tail with homology to the 5′ end of FRA2 Fragment C. FRA2 Fragment C was amplified with primer oBP600 (SEQ ID NO: 158), containing a 5′ tail with homology to the 3′ end of FRA2 Fragment U, and primer oBP601 (SEQ ID NO: 159). PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif.). FRA2 Fragment AB was created by overlapping PCR by mixing FRA2 Fragment A and FRA2 Fragment B and amplifying with primers oBP594 (SEQ ID NO: 152) and oBP597 (SEQ ID NO: 155). FRA2 Fragment UC was created by overlapping PCR by mixing FRA2 Fragment U and FRA2 Fragment C and amplifying with primers oBP598 (SEQ ID NO: 156) and oBP601 (SEQ ID NO: 159). The resulting PCR products were purified on an agarose gel followed by a Gel Extraction kit (Qiagen, Valencia, Calif.). The FRA2 ABUC cassette was created by overlapping PCR by mixing FRA2 Fragment AB and FRA2 Fragment UC and amplifying with primers oBP594 (SEQ ID NO: 152) and oBP601 (SEQ ID NO: 159). The PCR product was purified with a PCR Purification kit (Qiagen, Valencia, Calif.).

Competent cells of PNY1503 were made and transformed with the FRA2 ABUC PCR cassette using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.). Transformation mixtures were plated on synthetic complete media lacking uracil supplemented with 1% ethanol at 30° C. Transformants with a fra2 knockout were screened for by PCR with primers oBP602 (SEQ ID NO: 160) and oBP603 (SEQ ID NO: 161) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). A correct transformant was grown in YPE (yeast extract, peptone, 1% ethanol) and plated on synthetic complete medium containing 5-fluoro-orotic acid (0.1%) at 30° C. to select for isolates that lost the URA3 marker. The deletion and marker removal were confirmed by PCR with primers oBP602 (SEQ ID NO: 160) and oBP603 (SEQ ID NO: 161) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The absence of the FRA2 gene from the isolate was demonstrated by a negative PCR result using primers specific for the deleted coding sequence of FRA2, oBP605 (SEQ ID NO: 162) and oBP606 (SEQ ID NO: 163). The correct isolate was selected as strain CEN.PK 113-7D MATa ura3Δ::loxP his3Δ pdc6Δ pdc1Δ::P[PDC1]-DHAD|ilvD_Sm-PDC1t pdc5Δ::P[PDC5]-ADH|sadB_Ax-PDC5t gpd2Δ::loxP fra2Δ and designated as PNY1505 (BP1135).

ADH1 Deletion and kivD Ll(v) Integration

The ADH1 gene was deleted and replaced with the kivD coding region from Lactococcus lactis codon optimized for expression in Saccharomyces cerevisiae. The scarless cassette for the ADH1 deletion-kivD_Ll(y) integration was first cloned into plasmid pUC19-URA3MCS, as described in U.S. Provisional Application Ser. No. 61/356,379, filed Jun. 18, 2010, incorporated herein by reference. The vector is pUC19 based and contains the sequence of the URA3 gene from Saccharomyces cerevisiae CEN.PK 113-7D situated within a multiple cloning site (MCS). pUC19 contains the pMB1 replicon and a gene coding for beta-lactamase for replication and selection in Escherichia coli. In addition to the coding sequence for URA3, the sequences from upstream (250 bp) and downstream (150 bp) of this gene are present for expression of the URA3 gene in yeast.

The kivD coding region from Lactococcus lactis codon optimized for expression in Saccharomyces cerevisiae was amplified using pLH468 (U.S. Provisional Application Ser. No. 61/246,709, filed Sep. 29, 2009) as template with primer oBP562 (SEQ ID NO: 164), containing a PmeI restriction site, and primer oBP563 (SEQ ID NO: 165), containing a 5′ tail with homology to the 5′ end of ADH1 Fragment B. ADH1 Fragment B was amplified from genomic DNA prepared as above with primer oBP564 (SEQ ID NO: 166), containing a 5′ tail with homology to the 3′ end of kivD_Ll(y), and primer oBP565 (SEQ ID NO: 167), containing a Fsel restriction site. PCR products were purified with a PCR Purification kit (Qiagen, Valencia, Calif.). kivD_Ll(y)-ADH1 Fragment B was created by overlapping PCR by mixing the kivD_Ll(y) and ADH1 Fragment B PCR products and amplifying with primers oBP562 (SEQ ID NO: 164) and oBP565 (SEQ ID NO: 167). The resulting PCR product was digested with PmeI and FseI and ligated with T4 DNA ligase into the corresponding sites of pUC19-URA3MCS after digestion with the appropriate enzymes. ADH1 Fragment A was amplified from genomic DNA with primer oBP505 (SEQ ID NO: 168) containing a SacI restriction site, and primer oBP506 (SEQ ID NO: 169), containing an AscI restriction site. The ADH1 Fragment A PCR product was digested with SacI and AscI and ligated with T4 DNA ligase into the corresponding sites of the plasmid containing kivD_Ll(y)-ADH1 Fragment B. ADH1 Fragment C was amplified from genomic DNA with primer oBP507 (SEQ ID NO: 170), containing a PacI restriction site, and primer oBP508 (SEQ ID NO: 171), containing a SalI restriction site. The ADH1 Fragment C PCR product was digested with PacI and SalI and ligated with T4 DNA ligase into the corresponding sites of the plasmid containing ADH1 Fragment A-kivD_Ll(y)-ADH1 Fragment B. The hybrid promoter UAS(PGK1)-P_(FBA1) was amplified from vector pRS316-UAS(PGK1)-P_(FBA1)-GUS (SEQ ID NO: 172) with primer oBP674 (SEQ ID NO: 173), containing an AscI restriction site, and primer oBP675 (SEQ ID NO: 174), containing a PmeI restriction site. The UAS(PGK1)-P_(FBA1) PCR product was digested with AscI and PmeI and ligated with T4 DNA ligase into the corresponding sites of the plasmid containing kivD_Ll(y)-ADH1 Fragments ABC. The entire integration cassette was amplified from the resulting plasmid with primers oBP505 (SEQ ID NO: 168) and oBP508 (SEQ ID NO: 171) and purified with a PCR Purification kit (Qiagen, Valencia, Calif.).

Competent cells of PNY1505 were made and transformed with the ADH1-kivD_Ll(y) PCR cassette constructed above using a Frozen-EZ Yeast Transformation II™ kit (Zymo Research Corporation, Irvine, Calif.). Transformation mixtures were plated on synthetic complete media lacking uracil supplemented with 1% ethanol at 30° C. Transformants were grown in YPE (1% ethanol) and plated on synthetic complete medium containing 5-fluoro-orotic acid (0.1%) at 30° C. to select for isolates that lost the URA3 marker. The deletion of ADH1 and integration of kivD_Ll(y) were confirmed by PCR with external primers oBP495 (SEQ ID NO: 175) and oBP496 (SEQ ID NO: 176) and with kivD_Ll(y) specific primer oBP562 (SEQ ID NO: 164) and external primer oBP496 (SEQ ID NO: 176) using genomic DNA prepared with a Gentra® Puregene® Yeast/Bact. kit (Qiagen, Valencia, Calif.). The correct isolate was selected as strain CEN.PK 113-7D MATa ura3Δ::loxP his3Δ pdc6Δ pdc1Δ::P[PDC1]-DHAD|ilvD_Sm-PDC1tpdc5Δ::P[PDC5]-ADH|sadB_Ax-PDC5t gpd2Δ::loxP fra2Δ adh1Δ::UAS(PGK1)P[FBA1]-kivD_Ll(y)-ADH1t and designated as PNY1507 (BP1201). PNY1507 was transformed with isobutanol pathway plasmids pYZ090 (SEQ ID NO: 1) and pBP915 (described below).

Construction of the pRS316-UAS(PGK1)-FBA1p-GUS Vector

To clone a cassette UAS(PGK1)-FBA1p (SEQ ID NO: 177, first a 602 bp FBA1 promoter (FBA1p) was PCR-amplified from genomic DNA of CEN.PK with primers T-FBA1(SalI) (SEQ ID NO: 178) and B-FBA1(SpeI) (SEQ ID NO: 179), and cloned into SalI and SpeI sites on the plasmid pWS358-PGK1 p-GUS (SEQ ID NO: 180) after the PGK1p promoter was removed with a SalI/SpeI digest of the plasmid, yielding pWS358-FBA1p-GUS. The pWS358-PGK1 p-GUS plasmid was generated by inserting a PGK1p and beta-glucuronidase gene (GUS) DNA fragments into multiple cloning site of pWS358, which was derived from pRS423 vector (Christianson, et al., Gene 110:119-122, 1992). Secondly, the resulting pWS358-FBA1p-GUS plasmid was digested with SalI and SacI, a DNA fragment containing a FBA1p promoter, GUS gene, and FBAt terminator gel-purified, and cloned into SalI/SacI sites on pRS316 to create pRS316-FBA1p-GUS. Thirdly, a 118 bp DNA fragment containing an upstream activation sequence (UAS) located between positions −519 and −402 upstream of the 3-phosphoglycerate kinase (PGK1) open reading frame, namely UAS(PGK1), was PCR-amplified from genomic DNA of CEN.PK with primers T-U/PGK1(KpnI) (SEQ ID NO: 181) and B-U/PGK1(SalI) (SEQ ID NO: 182). The PCR product was digested with KpnI and SalI and cloned into KpnI/SalI sites on pRS316-FBA1p-GUS to create pRS316-UAS(PGK1)-FBA1p-GUS.

Construction of integration vector pUC19-kan::pdc1::FBA-alsS::TRX1

The FBA-alsS-CYCt cassette was constructed by moving the 1.7 kb BbvCI/PacI fragment from pRS426::GPD::alsS::CYC (U.S. Patent Application Publication No. 2007/0092957) to pRS426::FBA::ILV5::CYC (U.S. Patent Application Publication No. 2007/0092957, previously digested with BbvCI/PacI to release the ILV5 gene). Ligation reactions were transformed into E. coli TOP10 cells and transformants were screened by PCR using primers N98SeqF1 (SEQ ID NO: 183) and N99SeqR2 (SEQ ID NO: 184). The FBA-alsS-CYCt cassette was isolated from the vector using BglII and NotI for cloning into pUC19-URA3::ilvD-TRX1 (as described in U.S. Provisional Application Ser. No. 61/356,379, filed Jun. 18, 2010, incorporated herein by reference, clone “B”) at the AflII site (Klenow fragment was used to make ends compatible for ligation). Transformants containing the alsS cassette in both orientations in the vector were obtained and confirmed by PCR using primers N98SeqF4 (SEQ ID NO: 185) and N1111 (SEQ ID NO: 186) for configuration “A” and N98SeqF4 (SEQ ID NO: 185) and N1110 (SEQ ID NO: 187) for configuration “B”. A geneticin selectable version of the “A” configuration vector was then made by removing the URA3 gene (1.2 kb NotI/NaeI fragment) and adding a geneticin cassette previously described (SEQ ID NO: 655 of U.S. Provisional Application Ser. No. 61/356,379, filed Jun. 18, 2010, incorporated herein by reference). Klenow fragment was used to make all ends compatible for ligation, and transformants were screened by PCR to select a clone with the geneticin resistance gene in the same orientation as the previous URA3 marker using primers BK468 (SEQ ID NO: 188) and N160SeqF5 (SEQ ID NO: 189). The resulting clone was called pUC19-kan::pdc1::FBA-alsS::TRX1 (clone A)(SEQ ID NO: 190).

The pUC19-kan::pdc1::FBA-alsS integration vector described above was linearized with PmeI and transformed into PNY1507 (described above). PmeI cuts the vector within the cloned pdc1-TRX1 intergenic region and thus, leads to targeted integration at that location (Rothstein, Methods Enzymol. 194:281-301, 1991). Transformants were selected on YPE plus 50 μg/ml G418. Patched transformants were screened by PCR for the integration event using primers N160SeqF5 (SEQ ID NO: 189) and oBP512 (SEQ ID NO: 47). Two transformants were tested indirectly for acetolactate synthase function by evaluating the strains ability to make isobutanol. To do this, additional isobutanol pathway genes were supplied on E. coli-yeast shuttle vectors (pYZ090ΔalsS and pBP915, described below). One clone, strain MATa ura3Δ::loxP his3Δ pdc6Δ pdc1Δ::P[PDC1]-DHAD|ilvD_Sm-PDC1t-pUC19-loxP-kanMX-loxP-P[FBA1]-ALSIalsS_Bs-CYC1 t pdc5Δ::P[PDC5]-ADH|sadB_Ax-PDC5t gpd2Δ::loxP fra2Δ adh1Δ::UAS(PGK1)P [FBA1]-kivD_Ll(y)-ADH1t was designated as PNY2204. PNY2205 is PNY2204 transformed with pYZ090ΔalsS and pBP915 plasmids.

Isobutanol Pathway Plasmids (pYZ090ΔalsS and pBP915)

pYZ090 (SEQ ID NO: 1) was digested with SpeI and NotI to remove most of the CUP1 promoter and all of the alsS coding sequence and CYC terminator. The vector was then self-ligated after treatment with Klenow fragment and transformed into E. coli Stbl3 cells, selecting for ampicillin resistance. Removal of the DNA region was confirmed for two independent clones by DNA sequencing across the ligation junction by PCR using primer N191 (SEQ ID NO: 191). The resulting plasmid was named pYZ090ΔalsS (SEQ ID NO: 192).

pBP915 was constructed from pLH468 (SEQ ID NO: 2; U.S. Provisional Application Ser. No. 61/246,709, filed Sep. 29, 2009) by deleting the kivD gene and 957 base pairs of the TDH3 promoter upstream of kivD. pLH468 was digested with Swal and the large fragment (12896 bp) was purified on an agarose gel followed by a Gel Extraction kit (Qiagen, Valencia, Calif.). The isolated fragment of DNA was self-ligated with T4 DNA ligase and used to transform electrocompetent TOP10 Escherichia coli (Invitrogen, Carlsbad, Calif.). Plasmids from transformants were isolated and checked for the proper deletion by restriction analysis with the Swal restriction enzyme. Isolates were also sequenced across the deletion site with primers oBP556 (SEQ ID NO: 193) and oBP561 (SEQ ID NO: 194). A clone with the proper deletion was designated pBP915 (pLH468EkivD)(SEQ ID NO: 195).

Construction of Strains NYLA74, NYLA83, and NYLA84

Insertion-inactivation of endogenous PDC1 and PDC6 genes of S. cerevisiae. PDC1, PDC5, and PDC6 genes encode the three major isozymes of pyruvate decarboxylase is described as follows:

Construction of pRS425::GPM-sadB

A DNA fragment encoding a butanol dehydrogenase (SEQ ID NO: 70) from Achromobacter xylosoxidans (disclosed in U.S. Patent Application Publication No. 2009/0269823) was cloned. The coding region of this gene called sadB for secondary alcohol dehydrogenase (SEQ ID NO: 69) was amplified using standard conditions from A. xylosoxidans genomic DNA, prepared using a Gentra® Puregene® kit (Qiagen, Valencia, Calif.) following the recommended protocol for gram negative organisms using forward and reverse primers N473 and N469 (SEQ ID NOs: 74 and 75), respectively. The PCR product was TOPO®-Blunt cloned into pCR®4 BLUNT (Invitrogen™, Carlsbad, Calif.) to produce pCR4Blunt::sadB, which was transformed into E. coli Mach-1 cells. Plasmid was subsequently isolated from four clones, and the sequence verified.

The sadB coding region was PCR amplified from pCR4Blunt::sadB. PCR primers contained additional 5′ sequences that would overlap with the yeast GPM1 promoter and the ADH1 terminator (N583 and N584, provided as SEQ ID NOs: 76 and 77). The PCR product was then cloned using “gap repair” methodology in Saccharomyces cerevisiae (Ma, et al., Gene 58:201-216, 1987) as follows. The yeast-E. coli shuttle vector pRS425::GPM::kivD::ADH which contains the GPM1 promoter (SEQ ID NO: 72), kivD coding region from Lactococcus lactis (SEQ ID NO: 71), and ADH1 terminator (SEQ ID NO: 73) (described in U.S. Patent Application Publication No. 2007/0092957 A1, Example 17) was digested with BbvCI and PacI restriction enzymes to release the kivD coding region. Approximately 1 g of the remaining vector fragment was transformed into S. cerevisiae strain BY4741 along with 1 g of sadB PCR product. Transformants were selected on synthetic complete medium lacking leucine. The proper recombination event, generating pRS425::GPM-sadB, was confirmed by PCR using primers N142 and N459 (SEQ ID NOs: 108 and 109).

Construction of pdc6:: PGPM1-sadB Integration Cassette and PDC6 Deletion:

A pdc6::PGPM1-sadB-ADH1t-URA3r integration cassette was made by joining the GPM-sadB-ADHt segment (SEQ ID NO: 79) from pRS425::GPM-sadB (SEQ ID NO: 78) to the URA3r gene from pUC19-URA3r. pUC19-URA3r (SEQ ID NO: 80) contains the URA3 marker from pRS426 (ATCC No. 77107) flanked by 75 bp homologous repeat sequences to allow homologous recombination in vivo and removal of the URA3 marker. The two DNA segments were joined by SOE PCR (as described by Horton, et al., Gene 77:61-68, 1989) using as template pRS425::GPM-sadB and pUC19-URA3r plasmid DNAs, with Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers 114117-11A through 114117A-11D (SEQ ID NOs: 81, 82, 83, and 84), and 114117-13A and 114117-13B (SEQ ID NOs: 85 and 86).

The outer primers for the SOE PCR (114117-13A and 114117-13B) contained 5′ and 3′ ˜50 bp regions homologous to regions upstream and downstream of the PDC6 promoter and terminator, respectively. The completed cassette PCR fragment was transformed into BY4700 (ATCC No. 200866) and transformants were maintained on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202). Transformants were screened by PCR using primers 112590-34G and 112590-34H (SEQ ID NOs: 87 and 88), and 112590-34F and 112590-49E (SEQ ID NOs: 89 and 90) to verify integration at the PDC6 locus with deletion of the PDC6 coding region. The URA3r marker was recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal was confirmed by patching colonies from the 5-FOA plates onto SD-URA media to verify the absence of growth. The resulting identified strain has the genotype: BY4700 pdc6::PGPM1-sadB-ADH1t.

Construction of pdc1:: PPDC1-ilvD Integration Cassette and PDC1 Deletion:

A pdc1:: PPDC1-ilvD-FBA1t-URA3r integration cassette was made by joining the ilvD-FBA1t segment (SEQ ID NO: 91) from pLH468 (SEQ ID NO: 2) to the URA3r gene from pUC19-URA3r by SOE PCR (as described by Horton, et al., Gene 77:61-68, 1989) using as template pLH468 and pUC19-URA3r plasmid DNAs, with Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers 114117-27A through 114117-27D (SEQ ID NOs: 111, 112, 113, and 114).

The outer primers for the SOE PCR (114117-27A and 114117-27D) contained 5′ and 3′ ˜50 bp regions homologous to regions downstream of the PDC1 promoter and downstream of the PDC1 coding sequence. The completed cassette PCR fragment was transformed into BY4700 pdc6::PGPM1-sadB-ADH1t and transformants were maintained on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202). Transformants were screened by PCR using primers 114117-36D and 135 (SEQ ID NOs: 92 and 93), and primers 112590-49E and 112590-30F (SEQ ID NOs: 90 and 94) to verify integration at the PDC1 locus with deletion of the PDC1 coding sequence. The URA3r marker was recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal was confirmed by patching colonies from the 5-FOA plates onto SD-URA media to verify the absence of growth. The resulting identified strain “NYLA67” has the genotype: BY4700 pdc6:: PGPM1-sadB-ADH1t pdc1:: PPDC1-ilvD-FBA1t.

HIS3 Deletion

To delete the endogenous HIS3 coding region, a his3::URA3r2 cassette was PCR-amplified from URA3r2 template DNA (SEQ ID NO: 95). URA3r2 contains the URA3 marker from pRS426 (ATCC No. 77107) flanked by 500 bp homologous repeat sequences to allow homologous recombination in vivo and removal of the URA3 marker. PCR was done using Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers 114117-45A and 114117-45B (SEQ ID NOs: 96 and 97) which generated a ˜2.3 kb PCR product. The HIS3 portion of each primer was derived from the 5′ region upstream of the HIS3 promoter and 3′ region downstream of the coding region such that integration of the URA3r2 marker results in replacement of the HIS3 coding region. The PCR product was transformed into NYLA67 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants were selected on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. Transformants were screened to verify correct integration by replica plating of transformants onto synthetic complete media lacking histidine and supplemented with 2% glucose at 30° C. The URA3r marker was recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal was confirmed by patching colonies from the 5-FOA plates onto SD-URA media to verify the absence of growth. The resulting identified strain, called NYLA73, has the genotype: BY4700 pdc6:: PGPM1-sadB-ADH1t pdc1:: PPDC1-ilvD-FBA1t Δhis3.

Construction of pdc5::kanMX Integration Cassette and PDC5 Deletion:

A pdc5::kanMX4 cassette was PCR-amplified from strain YLR134W chromosomal DNA (ATCC No. 4034091) using Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers PDC5::KanMXF and PDC5::KanMXR (SEQ ID NOs: 98 and 99) which generated a ˜2.2 kb PCR product. The PDC5 portion of each primer was derived from the 5′ region upstream of the PDC5 promoter and 3′ region downstream of the coding region such that integration of the kanMX4 marker results in replacement of the PDC5 coding region. The PCR product was transformed into NYLA73 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants were selected on YP media supplemented with 1% ethanol and geneticin (200 μg/mL) at 30° C. Transformants were screened by PCR to verify correct integration at the PDC locus with replacement of the PDC5 coding region using primers PDC5kofor and N175 (SEQ ID NOs: 100 and 101). The identified correct transformants have the genotype: BY4700 pdc6:: PGPM1-sadB-ADH1t pdc1:: PPDC1-ilvD-FBA1t Δhis3 pdc5::kanMX4. The strain was named NYLA74.

Plasmid vectors pRS423::CUP1-alsS+FBA-budA and pRS426::FBA-budC+GPM-sadB were transformed into NYLA74 to create a butanediol producing strain (NGCI-047).

Plasmid vectors pLH475-Z4B8 (SEQ ID NO: 140) and pLH468 were transformed into NYLA74 to create an isobutanol producing strain (NGCI-049).

Deletion of HXK2 (hexokinase II):

A hxk2::URA3r cassette was PCR-amplified from URA3r2 template (described above) using Phusion® DNA polymerase (New England BioLabs Inc., Ipswich, Mass.) and primers 384 and 385 (SEQ ID NOs: 102 and 103) which generated a ˜2.3 kb PCR product. The HXK2 portion of each primer was derived from the 5′ region upstream of the HXK2 promoter and 3′ region downstream of the coding region such that integration of the URA3r2 marker results in replacement of the HXK2 coding region. The PCR product was transformed into NYLA73 using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 201-202) and transformants were selected on synthetic complete media lacking uracil and supplemented with 2% glucose at 30° C. Transformants were screened by PCR to verify correct integration at the HXK2 locus with replacement of the HXK2 coding region using primers N869 and N871 (SEQ ID NOs: 104 and 105). The URA3r2 marker was recycled by plating on synthetic complete media supplemented with 2% glucose and 5-FOA at 30° C. following standard protocols. Marker removal was confirmed by patching colonies from the 5-FOA plates onto SD-URA media to verify the absence of growth, and by PCR to verify correct marker removal using primers N946 and N947 (SEQ ID NOs: 106 and 107). The resulting identified strain named NYLA83 has the genotype: BY4700 pdc6:: PGPM1-sadB-ADH1t pdc1:: PPDC1-ilvD-FBA1t Δhis3 Δhxk2.

Construction of pdc5::kanMX Integration Cassette and PDC5 Deletion:

A pdc5::kanMX4 cassette was PCR-amplified as described above. The PCR fragment was transformed into NYLA83, and transformants were selected and screened as described above. The identified correct transformants named NYLA84 have the genotype: BY4700 pdc6:: PGPM1-sadB-ADH1t pdc1:: PPDC1-ilvD-FBA1t Δhis3 Δhxk2 pdc5::kanMX4.

Plasmid vectors pLH468 and pLH532 were simultaneously transformed into strain NYLA84 (BY4700 pdc6::PGPM1-sadB-ADH1t pdc1::PPDC1-ilvD-FBA1t Δhis3 Δhxk2 pdc5::kanMX4) using standard genetic techniques (Methods in Yeast Genetics, 2005, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) and the resulting “butanologen NYLA84” was maintained on synthetic complete media lacking histidine and uracil, and supplemented with 1% ethanol at 30° C.

Expression Vector pLH468

The pLH468 plasmid (SEQ ID NO: 2) was constructed for expression of DHAD, KivD, and HADH in yeast and is described in U.S. Patent Application Publication No. 2009/0305363, herein incorporated by reference. pLH486 was constructed to contain: a chimeric gene having the coding region of the ilvD gene from Streptococcus mutans (nt position 3313-4849) expressed from the S. cerevisiae FBA1 promoter (nt 2109-3105) followed by the FBA1 terminator (nt 4858-5857) for expression of DHAD; a chimeric gene having the coding region of codon optimized horse liver alcohol dehydrogenase (nt 6286-7413) expressed from the S. cerevisiae GPM1 promoter (nt 7425-8181) followed by the ADH1 terminator (nt 5962-6277) for expression of ADH; and a chimeric gene having the coding region of the codon-optimized kivD gene from Lactococcus lactis (nt 9249-10895) expressed from the TDH3 promoter (nt 10896-11918) followed by the TDH3 terminator (nt 8237-9235) for expression of KivD.

Coding regions for Lactococcus lactis ketoisovalerate decarboxylase (KivD) and horse liver alcohol dehydrogenase (HADH) were synthesized by DNA2.0, Inc. (Menlo Park, Calif.) based on codons that were optimized for expression in Saccharomyces cerevisiae (SEQ ID NO: 71 and 118, respectively) and provided in plasmids pKivDy-DNA2.0 and pHadhy-DNA2.0. The encoded proteins are SEQ ID NOs: 117 and 119, respectively. Individual expression vectors for KivD and HADH were constructed. To assemble pLH467 (pRS426::PTDH3-kivDy-TDH3t), vector pNY8 (SEQ ID NO: 121; also named pRS426.GPD-ald-GPDt, described in U.S. Patent Application Publication No. 2008/0182308, Example 17, which is herein incorporated by reference) was digested with AscI and SfiI enzymes, thus excising the GPD promoter and the ald coding region. A TDH3 promoter fragment (SEQ ID NO: 122) from pNY8 was PCR amplified to add an AscI site at the 5′ end and an SpeI site at the 3′ end, using 5′ primer OT1068 and 3′ primer OT1067 (SEQ ID NOs: 123 and 124). The AscI/SfiI digested pNY8 vector fragment was ligated with the TDH3 promoter PCR product digested with AscI and SpeI, and the SpeI-SfiI fragment containing the codon optimized kivD coding region isolated from the vector pKivD-DNA2.0. The triple ligation generated vector pLH467 (pRS426::PTDH3-kivDy-TDH3t). pLH467 was verified by restriction mapping and sequencing.

pLH435 (pRS425::PGPM1-Hadhy-ADH1t) was derived from vector pRS425::GPM-sadB (SEQ ID NO: 78) which is described in U.S. Provisional Application Ser. No. 61/058,970, Example 3, which is herein incorporated by reference. pRS425::GPM-sadB is the pRS425 vector (ATCC No. 77106) with a chimeric gene containing the GPM1 promoter (SEQ ID NO: 72), coding region from a butanol dehydrogenase of Achromobacter xylosoxidans (sadB; DNA SEQ ID NO: 69; protein SEQ ID NO: 70: disclosed in U.S. Patent Application Publication No. 2009/0269823), and ADH1 terminator (SEQ ID NO: 73). pRS425::GPMp-sadB contains BbvI and PacI sites at the 5′ and 3′ ends of the sadB coding region, respectively. A NheI site was added at the 5′ end of the sadB coding region by site-directed mutagenesis using primers OT1074 and OT1075 (SEQ ID NOs: 126 and 127) to generate vector pRS425-GPMp-sadB-NheI, which was verified by sequencing. pRS425::PGPM1-sadB-NheI was digested with NheI and PacI to drop out the sadB coding region, and ligated with the NheI-PacI fragment containing the codon optimized HADH coding region from vector pHadhy-DNA2.0 to create pLH435.

To combine KivD and HADH expression cassettes in a single vector, yeast vector pRS411 (ATCC No. 87474) was digested with SacI and NotI, and ligated with the SacI-SalI fragment from pLH467 that contains the PTDH3-kivDy-TDH3t cassette together with the SalI-NotI fragment from pLH435 that contains the PGPM1-Hadhy-ADH1t cassette in a triple ligation reaction. This yielded the vector pRS411::PTDH3-kivDy-PGPM1-Hadhy (pLH441) which was verified by restriction mapping.

In order to generate a co-expression vector for all three genes in the lower isobutanol pathway: ilvD, kivDy, and Hadhy, pRS423 FBA ilvD(Strep) (SEQ ID NO: 128) which is described in U.S. Patent Application Publication No. 2010/0081154 as the source of the IlvD gene, was used. This shuttle vector contains an F1 origin of replication (nt 1423 to 1879) for maintenance in E. coli and a 2 micron origin (nt 8082 to 9426) for replication in yeast. The vector has an FBA1 promoter (nt 2111 to 3108; SEQ ID NO: 120) and FBA terminator (nt 4861 to 5860; SEQ ID NO: 129). In addition, it carries the His marker (nt 504 to 1163) for selection in yeast and ampicillin resistance marker (nt 7092 to 7949) for selection in E. coli. The ilvD coding region (nt 3116 to 4828; SEQ ID NO: 115; protein SEQ ID NO: 116) from Streptococcus mutans UA159 (ATCC No. 700610) is between the FBA promoter and FBA terminator forming a chimeric gene for expression. In addition, there is a lumio tag fused to the ilvD coding region (nt 4829-4849).

The first step was to linearize pRS423 FBA ilvD(Strep) (also called pRS423-FBA(SpeI)-IIvD(Streptococcus mutans)-Lumio) with SacI and SacII (with SacII site blunt ended using T4 DNA polymerase), to give a vector with total length of 9,482 bp. The second step was to isolate the kivDy-hADHy cassette from pLH441 with SacI and KpnI (with KpnI site blunt ended using T4 DNA polymerase), which gives a 6,063 bp fragment. This fragment was ligated with the 9,482 bp vector fragment from pRS423-FBA(SpeI)-IIvD(Streptococcus mutans)-Lumio. This generated vector pLH468 (pRS423::PFBA1-ilvD(Strep) Lumio-FBA1t-PTDH3-kivDy-TDH3t-PGPM1-hadhy-ADH it) which was confirmed by restriction mapping and sequencing.

pLH532 Construction

The pLH532 plasmid (SEQ ID NO: 130) was constructed for expression of ALS and KARI in yeast. pLH532 is a pHR81 vector (ATCC No. 87541) containing the following chimeric genes: 1) the CUP1 promoter (SEQ ID NO: 139), acetolactate synthase coding region from Bacillus subtilis (AIsS; SEQ ID NO: 137; protein SEQ ID NO: 138) and CYC1 terminator2 (SEQ ID NO: 133); 2) an ILV5 promoter (SEQ ID NO: 134), Pf5.IIvC coding region (SEQ ID NO: 132) and ILV5 terminator (SEQ ID NO: 135); and 3) the FBA1 promoter (SEQ ID NO: 136), S. cerevisiae KARI coding region (ILV5; SEQ ID NO: 131); and CYC1 terminator.

The Pf5.IIvC coding region is a sequence encoding KARI derived from Pseudomonas fluorescens that was described in U.S. Patent Application Publication No. 2009/0163376, which is herein incorporated by reference.

The Pf5.IIvC coding region was synthesized by DNA2.0, Inc. (Menlo Park, Calif.; SEQ ID NO: 132) based on codons that were optimized for expression in Saccharomyces cerevisiae.

pYZ090 Construction

pYZ090 (SEQ ID NO: 1) is based on the pHR81 (ATCC No. 87541) backbone and was constructed to contain a chimeric gene having the coding region of the alsS gene from Bacillus subtilis (nt position 457-2172) expressed from the yeast CUP1 promoter (nt 2-449) and followed by the CYC1 terminator (nt 2181-2430) for expression of ALS, and a chimeric gene having the coding region of the ilvC gene from Lactococcus lactis (nt 3634-4656) expressed from the yeast ILV5 promoter (2433-3626) and followed by the ILV5 terminator (nt 4682-5304) for expression of KARI.

pYZ067 Construction

pYZ067 was constructed to contain the following chimeric genes: 1) the coding region of the ilvD gene from S. mutans UA159 (nt position 2260-3971) expressed from the yeast FBA1 promoter (nt 1161-2250) followed by the FBA terminator (nt 4005-4317) for expression of dihydroxy acid dehydratase (DHAD), 2) the coding region for horse liver ADH (nt 4680-5807) expressed from the yeast GPM promoter (nt 5819-6575) followed by the ADH1 terminator (nt 4356-4671) for expression of alcohol dehydrogenase, and 3) the coding region of the KivD gene from Lacrococcus lactis (nt 7175-8821) expressed from the yeast TDH3 promoter (nt 8830-9493) followed by the TDH3 terminator (nt 5682-7161) for expression of ketoisovalerate decarboxylase.

pRS423::CUP1-alsS+FBA-budA and pRS426::FBA-budC+GPM-sadB and pLH475-Z4B8 Construction

Construction of pRS423::CUP1-alsS+FBA-budA and pRS426::FBA-budC+GPM-sadB and pLH475-Z4B8 is described in U.S. Patent Application Publication No. 2009/0305363, incorporated herein by reference.

Construction of Saccharomyces cerevisiae Strain PNY2242

Strain PNY2242 was constructed in several steps from PNY1507 (described above). First, a chimeric gene comprised of the FBA1 promoter, the aIsS coding region, and the CYC1 terminator was integrated into Chromosome XII, upstream of the TRX1 gene. The sequence of the modified locus is provided as SEQ ID NO: 196. Next, two copies of a gene encoding horse liver alcohol dehydrogenase were integrated into Chromosomes VII and XVI. On Chromosome VII, a chimeric gene comprised of the PDC1 promoter, the hADH coding region, and the ADH1 terminator were placed into the fra2Δ locus (the original deletion of FRA2 is described above). The sequence of the modified locus is provided as SEQ ID NO: 197. On Chromosome XVI, a chimeric gene comprised of the PDC5 promoter, the hADH coding region, and the ADH1 terminator were integrated in the region formerly occupied by the long term repeat element YPRCdelta15. The sequence of the modified locus is provided as SEQ ID NO: 198. Then the native genes YMR226c and ALD6 were deleted. Elimination of YMR226c was a scarless deletion of only the coding region. The sequence of the modified locus is provided as SEQ ID NO: 199. The ALD6 coding region plus 700 bp of upstream sequence were deleted using CRE-lox mediated marker removal (methodology described above), so the resulting locus contains one loxP site. The sequence of the modified locus is provided as SEQ ID NO: 200. Finally, plasmids were introduced into the strain for expression of KARI (pLH702, SEQ ID NO: 201) and DHAD (pYZ067DkivDDhADH, SEQ ID NO: 202), resulting in strain PNY2242.

Where the recombinant microorganism produces isobutanol, under certain embodiments, smicroorganisms show higher specific productivity. Further, the volumetric rate was improved by about 50%.

While not wishing to be bound by theory, it is believed that the methods described herein provide extractive fermentation methods with improved production yields of product alcohol. As discussed above, alcohol production utilizing fermentation by microorganisms may be inefficient due to the alcohol toxicity thresholds of the microorganism. In some embodiments, the methods herein provide a means to convert the product alcohol into a substance less toxic to the microorganism. For example, the product alcohol may be contacted with carboxylic acid in the presence of a catalyst which esterifies the alcohol with the carboxylic acid and thereby, produces alcohol esters which are less toxic to the microorganism. In addition, the generation of alcohol esters from the product alcohol results in a lower concentration of the product alcohol in the fermentation medium. The reduced concentration of product alcohol minimizes the toxic effects of the product alcohol on the microorganism and thus, leads to improved production yields of product alcohol.

Carboxylic acid may serve as an extractant, and alcohol esters can partition into the extractant. However, the partition coefficient of the extractant may be degraded by lipid contamination. To reduce the degradation of the partition coefficient of the extractant, lipids present in the fermentation medium may be converted to extractant and consequently, minimize lipid contamination. In some embodiments, the methods herein provide a means to convert the lipids present in the feedstock or biomass into an extractant by catalytically hydrolyzing the lipids to carboxylic acid. The carboxylic acid produced by this hydrolysis may serve as an extractant or esterified with the product alcohol to form alcohol esters. Thus, the methods described herein provide a means to preserve the partition coefficient of the extractant (e.g., lipid hydrolysis) as well as minimize the toxic effects of the product alcohol (e.g., esterification of the product alcohol.

Carboxylic acid may be supplied to the fermentation vessel or derived by hydrolysis from lipids (e.g., biomass) supplied to the fermentation vessel. The amount of carboxylic acid should be sufficient to form a two-phase mixture comprising an organic phase and an aqueous phase. That is, carboxylic acid (i.e., extractant) in an appropriate concentration contacts the fermentation broth and forms the two-phase mixture. The alcohol esters formed in the fermentation broth will preferentially partition into the organic phase because these esters are formed at a concentration in excess of the equilibrium concentration of the aqueous phase. The alcohol ester-containing organic phase may be separated from the fermentation broth, the product alcohol may be recovered from organic phase, and the extractant may be recycled to the fermentation vessel.

Recovery of Diols Using Enzymatyic Production of Diol Esters.

Alcohols that are diols may be produced in fermentation using microorganisms that either naturally produce diols or are genetically engineered to produce diols. Materials and processes described above for production, separation, hydrolysis, and recovery of alcohols, such as butanol, apply to the present methods for producing and recovering diols with the substitution of a microorganism that can produce a diol in fermentation as described below. Feedstocks and feedstock preparation, including oil stream separation and oil conversion to carboxylic acid which may be used in esterification and extraction, as well as solids separation, are all as described above. In addition, production of glycerol as a by-product of acyl glyceride hydrolysis is as described above. Glycerol may be used in fermentation medium as a carbon source and/or as an intermediated in production of a diol, such as described below in production of 1,3-PDO.

In addition, esterification of a diol with a carboxylic acid in the present method may occur following fermentative production of the diol. The fermentative microorganism may not have a low toxicity threshold for the diol produced, which is the case described above for butanol, and thus removal of the diol during fermentation would not be needed. The esterification may be performed in a fermentation product broth that is derived from a fermentation medium. The fermentation product broth is a spent fermentation medium in that fermentation has occurred whereby sugars (or other carbohydrate source) in the fermentation medium have been substantially metabolized and there is little more diol product being made. In some embodiments, the fermentation product broth may be processed to remove cells of the fermentative microorganism by a method not limited to centrifugation, ultrafiltration, flocculation or decantation prior to esterification of the diol. In some embodiments, undissolved solids may be removed prior to esterification using methods known to those skilled in the art, such as those above. In some embodiments protease activity may be reduced, including where no protease activity remains, Protease activity may be reduced by methods known to one skilled in the art such as using protease inhibitors, heating to inactivate proteases, and adding a protease that digests other proteases but not itself and the lipase (see for example Matsushim, K., Biochem. Biophys. Res. Comm., 90, (4), (1979) p 1142 and Scheiper et al., Bioorganic & Medical Chemistry Letters, 21 (2011), p 5480).

Esterification of a diol may produce a diol monoester, a diol diester, or a mixture of diol monoesters and diol diesters.

Also in addition to previously described processes, an organic solvent is present during esterification in a concentration that is sufficient to produce a two-phase mixture with the fermentation medium or fermentation product broth. The organic solvent may be the carboxylic acid used in the esterification reaction, or it may contain the carboxylic acid as well as at least one non-reactive organic solvent. The non-reactive organic solvent is one that would not participate in an esterification reaction between a carboxylic acid and an alcohol to produce a carboxylic acid alcohol ester. The diol ester product (including monoesters, and/or diesters) will partition to the organic phase, which is separated from the aqueous phase of the two-phase mixture. The diol ester is hydrolyzed and the diol recovered as described above for alcohols and butanol.

Diol Containing Compositions

The present invention is also directed to compositions containing diols produced by fermentation as well as diol esters produced to facilitate diol recovery from fermentation medium or fermentation product broth. In one embodiment the composition is a fermentation broth that contains a microorganism capable of producing a product diol, fermentable sugars, a product diol, at least one carboxylic acid, a catalyst capable of extracellularly esterifying a carboxylic acid with the product diol into carboxylic acid diol esters, and carboxylic acid diol esters (including diol monoesters and/or diol diesters). In this composition fermentation is active and the diol is being produced by the microorganism, while concurrently the produced diol is esterified with the carboxylic acid by the catalyst. This composition may also contain oil containing glycerides which may be hydrolyzed by the catalyst to produce free fatty acids, or which may be transesterified by the catalyst to produce fatty acid diol esters. The oil, carboxylic acid (e.g. fatty acid), and fermentable sugars may all be derived from a biomass. There may be additional components in the composition.

In another embodiment the composition is a fermentation product broth that contains a product diol, at least one carboxylic acid, a catalyst capable of extracellularly esterifying a carboxylic acid with said product diol into carboxylic acid diol esters, and carboxylic acid diol esters. In this composition fermentation is substantially complete and the product diol is esterified with the carboxylic acid by the catalyst following fermentation, in the fermentation product broth. This composition may also contain oil containing glycerides which may be hydrolyzed by the catalyst to produce free fatty acids. The oil and carboxylic acid (e.g. fatty acid) may all be derived from a biomass. There may be additional components in the composition.

The present compositions in some embodiments contain an organic solvent in addition to the carboxylic acid and oil that creates a two-phase mixture wherein the diol ester partitions between the aqueous phase and the organic phase.

Microorganisms for Diol Production

Any microorganism that is capable of producing a diol either naturally or through genetic metabolic engineering of a diol biosynthetic pathway may be used in the present methods. Some examples thereof are given below.

1,2-PDO is produced naturally by a variety of bacteria. 1,2-PDO formation was observed in the genera Clostridium (e.g. Clostridium thermobutyricum), Escherichia (e.g. Escherichia coli), Bacteroides (e.g. Bacteroides ruminicola), as well as in yeasts (Bennett et al. Appl Microbiol Biotechnol 55:1-9 (2001)). The biosynthesis of 1,2-PDO is through two main routes, one in which deoxy sugars are used as the carbon source (and in this route the key intermediate, lactaldehyde, is formed directly from a glycolytic reaction) while in the other route conversion of the glycolytic intermediate, dihydroxyacetone phosphate, to methylgloxal is the crucial branch. Subsequent reduction of methylglyoxal can yield 1,2-propanediol (Bennett et al. Appl Microbiol Biotechnol 55: 1-9 2001). Recent progress in metabolic engineering of 1,2-PDO producing strains, to enhance natural production, is described e.g. by Cameron et al. (Cameron et al. Biotechnol Prog 14: 116-25 1998) and Bennett and San (Bennett et al. Appl Microbiol Biotechnol 55: 1-9 2001).

Though no organism is known that can ferment sugars directly to 1,3-PDO (Cameron et al. Biotechnol. Prog. 14: 116-25 (1998)), natural producers of 1,3-PDO from glycerol are of the genera Klebsiella, Citrobacter, Enterobacter and Lactobacilli (Saxena et al. Biotechnol. Adv. 27: 895-913 2009). Usually the biosynthesis of 1,3-PDO from glycerol comprises two reaction steps: a glycerol dehydratase catalyzes the conversion of glycerol to 3-hydroxypropionaldehyde, which is subsequently reduced to 1,3-PDO in a 1,3-PDO oxidorectase reaction. Recent progress in metabolic engineering of 1,3-PDO producing strains utilizing several substrates is described e.g. by Nakamura et al. (Curr. Opin. Biotechnol. 14: 454-9 (2003)) and by Saxena et al. (Biotechnol Adv 27: 895-913 (2009)). Strains of E. coli that have been engineered for production of 1,3-PDO are disclosed, for example, in U.S. Pat. No. 7,504,250, U.S. Pat. No. 7,629,161, U.S. Pat. No. 7,005,291, and U.S. Pat. No. 6,013,494.

As disclosed in WO2011/047101, enzymes expressed in E. coli to create a BDO biosynthetic pathway include CoA-dependent succinic semialdehyde dehydrogenase, 4-hydroxybutanoate dehydrogenase, alpha-ketoglutarate decarboxylase, 4-hydroxybutyryl CoA:acetyl-CoA transferase, butyrate kinase, phosphotransbutyrylase, aldehyde dehydrogenase, and alcohol dehydrogenase. Microorganisms genetically engineered to produce PDO are described in U.S. Pat. No. 6,013,494, U.S. Pat. No. 6,514,733, U.S. Pat. No. 7,504,250, U.S. Pat. No. 7,629,161, and U.S. Pat. No. 7,005,291.

Metabolism of 1,2-EDO is known to occur in microorgansims such as those belonging to Enterobacteriacae, e.g. Aerobacter aerogenes (Toraya et al. J. Bacteriol. 139: 39-47 (1979)) and Clostridiaceae, e.g. Chlostridium glycolicum (Gaston et al. J. Bacteriol. 85: 356-62 (1963)). One key enzyme in the pathway is lactaldehyde reductase (EC:1.1.1.77) that catalyzes the conversion of glycolaldehyde to 1,2-EDO. Glycolaldehyde can be interconverted to glycolate in a reversible reaction. Glycolate on the other hand can be derived from glycerate or phosphoglycolate. However, only catabolism of 1,2-EDO but no relevant biotechnological production is so far described, corresponding to the preference of lactaldehyde reductase to convert 1,2 EDO into glycolaldehyde (Boronat et al. J Bacteriol 140: 320-6 1979). This directionality is exploited for e.g. the production of glycolic acid from-1,2-EDO (Wei et al. J. Ind. Microbiol. Biotechnol. 36: 1029-34 (2009)).

2,3-BDO synthesis is part of a mixed acid fermentation pathway in anaerobic or microaerobic growth of different microorganisms. In addition to 2,3-BDO other end-products are formed, such as ethanol, acetate, lactate, formate and succinate, depending on the microorganisms and the cultivation conditions applied (Zeng et al. Curr. Opin. Biotechnol. 22: 749-757 (2011)). Natural bacterial producers are, for example, found in the genera of Klebsiella (e.g. K. oxytoca; Ji et al. Biotechnol. Lett. 30: 731-4 (2008); Ma et al. Appl. Microbiol. Biotechnol. 82: 49-57 (2009)), Serratia (e.g. S. marcescens; Zhang et al. J. Ind. Microbiol. Biotechnol. 37: 857-862 (2010)), Brevibacterium (e.g. B. saccharolyticum; Takusagawa et al. Biosci. Biotechnol. Biochem. 65: 1876-8 (2001)), Corynebacterium (e.g. C. variabile; Starrenburg et al. Appl. Environ. Microbiol. 57: 3535-3540 (1991)), Enterobacter (e.g. E. aerugenes; Barrett et al. J. Dairy. Sci. 66: 2507-14 (1983)), Pseudomonas (e.g. P. chlororaphis; Cho et al. Mol. Plant Microbe Interact. 21: 1067-75 (2008)), Lactobacillus (Ferain et al. J. Bacteriol. 178: 7311-5 (1996)), Lactococcus (Starrenburg et al. Appl. Environ. Microbiol. 57: 3535-3540 (1991)), Leuconostoc (Starrenburg et al. Appl. Environ. Microbiol. 57: 3535-3540 (1991)), Bacillus (e.g. B. polymyxa; Laube et al. Biotechnology Letters 6: 257-262 (1984)), and Clostridium (Kopke et al. Appl. Environ. Microbiol. 77: 5467-75 (2011)) as well as in yeasts (Romano et al. Int. J. Food Microbiol. 86: 163-8 (2003)). Biosynthesis of 2,3-BDO from the metabolic intermediate pyruvic acid typically involves at least three steps. Pyruvic acid is converted to acetolactate, which is decarboxylated to acetoin. Alternatively pyruvic acid reacts to diacetyl, which is subsequently reduced to acetoin. Finally acetoin is reduced to butanediol (van Leeuwenhoek 49: 209-224 (1983); Syu, Appl. Microbiol. Biotechnol. 55: 10-8 (2001)). Metabolic engineering was successfully applied for improving or newly creating highly efficient and/or stereo-selective 2,3-BDO producing organisms, such as Clostridium acetobutylicum (Siemerink et al. Appl. Environ. Microbiol. 77: 2582-2588 (2011)), Escherichia coli (Ui, J. of Fermentation Technology 84: 185 (1997); Yan et al. Org. Biomol. Chem. 7: 3914-7 (2009); Nielsen et al. Biotechnol. J. 5: 274-284 (2010)), and Lactococcus lactis (Gaspar et al. Appl. Environ. Microbiol. 77: 6826-6835 (2011)).

Successful metabolic engineering of E. coli to produce 1,4-BDO was reported (Yim et al. Nat. Chem. Biol. 7: 445-52 (2011)). Two 1,4-BDO biosynthetic pathways were introduced starting from succinyl semialdehyde derived from intermediates of central carbon metabolism, either from alpha-ketoglutaric acid or alternatively from succinate via succinyl-CoA. Succinyl semialdehyde is subsequently reduced to 4-hydroxybutyric acid, 4-hydroxybutyric acid is reacted with acetyl-CoA to form acetic acid and 4-hydroxybutyryl CoA, 4-hydroxybutyryl-CoA finally is converted to 1,4-BDO via 4-hydrxybutyraldehyde in two reductive steps, coupled with the loss of CoA.

Production of diols by fermentation using microorganisms may be performed as known to one skilled in the art. For example, production of 2,3-butanediol using a genetically engineered strain of Sacharomyces cerevisiae is described in US 2009/0305363, which is incorporated herein by reference. Production of 1,3-propanediol using genetically engineered strains of E. coli is described in U.S. Pat. No. 7,504,250; U.S. Pat. No. 7,629,161, U.S. Pat. No. 7,005,291, and U.S. Pat. No. 6,013,494.

Further, while various embodiments of the present invention have been described above, it should be understood that they have been presented by way of example only, and not limitation. It will be apparent to persons skilled in the relevant art that various changes in form and detail can be made therein without departing from the spirit and scope of the invention. Thus, the breadth and scope of the present invention should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the claims and their equivalents.

All publications, patents, and patent applications mentioned in this specification are indicative of the level of skill of those skilled in the art to which this invention pertains, and are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

EXAMPLES

The following nonlimiting examples will further illustrate the invention. It should be understood that, while the following examples involve corn as feedstock and COFA as carboxylic acid, other biomass sources can be used for feedstock and acids other than COFA can serve as carboxylic acid, without departing from the present invention. Moreover, while the following examples involve butanol and butyl ester production, other alcohols including ethanol, and alcohol esters can be produced without departing from the present invention.

While various embodiments of the present invention have been described above, it should be understood that they have been presented by way of example only, and not limitation. It will be apparent to persons skilled in the relevant art that various changes in form and detail can be made therein without departing from the spirit and scope of the invention. Thus, the breadth and scope of the present invention should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the following claims and their equivalents.

As used herein, the meaning of abbreviations used was as follows: “g” means gram(s), “kg” means kilogram(s), “L” means liter(s), “mL” means milliliter(s), “μL” means microliter(s), “mL/L” means milliliter(s) per liter, “mL/min” means milliliter(s) per min, “DI” means deionized, “uM” means micrometer(s), “nm” means nanometer(s), “w/v” means weight/volume, “OD” means optical density, “OD₆₀₀” means optical density at a wavelength of 600 nM, “dcw” means dry cell weight, “rpm” means revolutions per minute, “° C.” means degree(s) Celsius, “° C./min” means degrees Celsius per minute, “slpm” means standard liter(s) per minute, “ppm” means part per million, “pdc” means pyruvate decarboxylase enzyme followed by the enzyme number.

General Methods

Seed Flask Growth

A Saccharomyces cerevisiae strain that was engineered to produce isobutanol from a carbohydrate source, with pdc1 deleted, pdc5 deleted, and pdc6 deleted, was grown to 0.55-1.1 g/L dcw (OD₆₀₀ 1.3-2.6—Thermo Helios α Thermo Fisher Scientific Inc., Waltham, Mass.) in seed flasks from a frozen culture. The culture was grown at 23-26° C. in an incubator rotating at 300 rpm. The frozen culture was previously stored at −80° C. The composition of the first seed flask medium was:

-   -   3.0-5.0 g/L dextrose     -   3.0-3.5 g/L ethanol, anhydrous     -   3.7 g/L ForMedium™ Synthetic Complete Amino Acid (Kaiser)         Drop-Out: without HIS, without URA (Reference # DSCK162CK)     -   6.7 g/L Difco Yeast Nitrogen Base without amino acids (No.         291920).

Eight to twelve milliliters from the first seed flask culture was transferred to a 2 L flask and grown at 30° C. in an incubator rotating at 300 rpm. The second seed flask has 220 mL of the following medium:

30.0 g/L dextrose

5.0 g/L ethanol, anhydrous

3.7 g/L ForMedium™ Synthetic Complete Amino Acid (Kaiser) Drop-Out:

without HIS, without URA (Reference # DSCK162CK)

6.7 g/L Difco Yeast Nitrogen Base without amino acids (No. 291920)

0.2 M MES Buffer titrated to pH 5.5-6.0.

The culture was grown to 0.55-1.1 g/L dcw (OD₆₀₀ 1.3-2.6). An addition of 30 mL of a solution containing 200 g/L peptone and 100 g/L yeast extract was added at this cell concentration. Then, an addition of 250-300 mL of 0.2 uM filter sterilized HD OCENOL® 90/95 oleyl alcohol (Cognis, Monheim, Del.) was added to the flask. The culture continues to grow to >4 g/L dcw (OD₆₀₀>10) before being harvested and added to the fermentation.

Fermentation Preparation

Initial Fermentation Vessel Preparation

A glass jacked, 2 L fermentation vessel (Sartorius AG, Goettingen, Germany) was charged with house water to 66% of the liquefaction weight. A pH probe (Hamilton Easyferm Plus K8, part number: 238627, Hamilton Bonaduz AG, Bonaduz, Switzerland) was calibrated through the Sartorius DCU-3 Control Tower Calibration menu. The zero was calibrated at pH=7. The span was calibrated at pH=4. The probe was then placed into the fermentation vessel through the stainless steel head plate. A dissolved oxygen probe (pO₂ probe) was also placed into the fermentation vessel through the head plate. Tubing used for delivering nutrients, seed culture, extracting solvent, and base were attached to the head plate and the ends were foiled. The entire fermentation vessel was placed into a Steris (Steris Corporation, Mentor, Ohio) autoclave and sterilized in a liquid cycle for 30 minutes.

The fermentation vessel was removed from the autoclave and placed on a load cell. The jacket water supply and return line was connected to the house water and clean drain, respectively. The condenser cooling water in and water out lines were connected to a 6-L recirculating temperature bath running at 7° C. The vent line that transfers the gas from the fermentation vessel was connected to a transfer line that was connected to a Thermo mass spectrometer (Prima dB, Thermo Fisher Scientific Inc., Waltham, Mass.). The sparger line was connected to the gas supply line. The tubing for adding nutrients, extract solvent, seed culture, and base was plumbed through pumps or clamped closed.

The fermentation vessel temperature was controlled at 55° C. with a thermocouple and house water circulation loop. Wet corn kernels (#2 yellow dent) were ground using a hammer mill with a 1.0 mm screen, and the resulting ground whole corn kernels were then added to the fermentation vessel at a charge that was 29-30% (dry corn solids weight) of the liquefaction reaction mass.

Lipase Treatment Pre-Liquefaction

A lipase enzyme stock solution was added to the fermentation vessel to a final lipase concentration of 10 ppm. The fermentation vessel was held at 55° C., 300 rpm, and 0.3 slpm N₂ overlay for >6 hrs. After the lipase treatment was complete, liquefaction was performed as described below (Liquefaction).

Liquefaction

An alpha-amylase was added to the fermentation vessel per its specification sheet while the fermentation vessel was mixing at 300-1200 rpm, with sterile, house N₂ being added at 0.3 slpm through the sparger. The temperature set-point was changed from 55° C. to 85° C. When the temperature was >80° C., the liquefaction cook time was started and the liquefaction cycle was held at >80° C. for 90-120 minutes. The fermentation vessel temperature set-point was set to the fermentation temperature of 30° C. after the liquefaction cycle was complete. N₂ was redirected from the sparger to the head space to prevent foaming without the addition of a chemical antifoaming agent.

Lipase Treatment Post-Liquefaction

The fermentation vessel temperature was set to 55° C. instead of 30° C. after the liquefaction cycle was complete (Liquefaction). The pH was manually controlled at pH=5.8 by making bolus additions of acid or base when needed. A lipase enzyme stock solution was added to the fermentation vessel to a final lipase concentration of 10 ppm. The fermentation vessel was held at 55° C., 300 rpm, and 0.3 slpm N₂ overlay for >6 hrs. After the Lipase Treatment was complete, the fermentation vessel temperature was set to 30° C.

Lipase Heat Inactivation Treatment (Heat Kill Treatment Method)

The fermentation vessel temperature was held at >80° C. for >15 minutes to inactivate the lipase. After the Heat Inactivation Treatment was complete, the fermentation vessel temperature was set to 30° C.

Nutrient Addition Prior to Inoculation

Ethanol (7 mL/L, post-inoculation volume, 200 proof, anhydrous) was added to the fermentation vessel just prior to inoculation. Thiamine was added to a final concentration of 20 mg/L and 100 mg/L nicotinic acid was also added just prior to inoculation.

Oleyl Alcohol or Corn Oil Fatty Acids Addition Prior to Inoculation

Added 1 L/L (post-inoculation volume) of oleyl alcohol or corn oil fatty acids immediately after inoculation.

Fermentation Operation

Fermentation Vessel Inoculation

The fermentation vessels pO₂ probe was calibrated to zero while N₂ was being added to the fermentation vessel. The fermentation vessels pO₂ probe was calibrated to its span with sterile air sparging at 300 rpm. The fermentation vessel was inoculated after the second seed flask with >4 g/L dcw. The shake flask was removed from the incubator/shaker for 5 minutes allowing a phase separation of the oleyl alcohol phase and the aqueous phase. The aqueous phase (110 mL) was transferred to a sterile, inoculation bottle. The inoculum was pumped into the fermentation vessel through a peristaltic pump.

Fermentation Vessel Operating Conditions

The fermentation vessel was operated at 30° C. for the entire growth and production stages. The pH was allowed to drop from a pH between 5.7-5.9 to a control set-point of 5.2 without adding any acid. The pH was controlled for the remainder of the growth and production stage at a pH=5.2 with ammonium hydroxide. Sterile air was added to the fermentation vessel, through the sparger, at 0.3 slpm for the remainder of the growth and production stages. The pO₂ was set to be controlled at 3.0% by the Sartorius DCU-3 Control Box PID control loop, using stir control only, with the stirrer minimum being set to 300 rpm and the maximum being set to 2000 rpm. The glucose was supplied through simultaneous saccharification and fermentation of the liquified corn mash by adding a α-amylase (glucoamylase). The glucose was kept excess (1-50 g/L) for as long as starch was available for saccharification.

Analytical

Gas Analysis

Process air was analyzed on a Thermo Prima (Thermo Fisher Scientific Inc., Waltham, Mass.) mass spectrometer. This was the same process air that was sterilized and then added to each fermentation vessel. Each fermentation vessel's off-gas was analyzed on the same mass spectrometer. This Thermo Prima dB has a calibration check run every Monday morning at 6:00 am. The calibration check was scheduled through the Gas Works v1.0 (Thermo Fisher Scientific Inc., Waltham, Mass.) software associated with the mass spectrometer. The gas calibrated for were:

Calibration GAS Concentration mole % Cal Frequency Nitrogen 78% weekly Oxygen 21% weekly Isobutanol 0.2%  yearly Argon  1% weekly Carbon Dioxide 0.03%  weekly

Carbon dioxide was checked at 5% and 15% during calibration cycle with other known bottled gases. Oxygen was checked at 15% with other known bottled gases. Based on the analysis of the off-gas of each fermentation vessel, the amount of isobutanol stripped, oxygen consumed, and carbon dioxide respired into the off-gas was measured by using the mass spectrometer's mole fraction analysis and gas flow rates (mass flow controller) into the fermentation vessel. Calculate the gassing rate per hour and then integrating that rate over the course of the fermentation.

Cell Mass Measurement

A 0.08% Trypan Blue solution was prepared from a 1:5 dilution of 0.4% Trypan Blue in NaCl (VWR BDH8721-0) with 1×PBS. A 1.0 mL sample was pulled from a fermentation vessel and placed in a 1.5 mL Eppendorf centrifuge tube and centrifuged in an Eppendorf, 5415C at 14,000 rpm for 5 minutes. After centrifugation, the top solvent layer was removed with an m200 Variable Channel BioHit pipette with 20-200 μL BioHit pipette tips. Care was made not to remove the layer between the solvent and aqueous layers. Once the solvent layer was removed, the sample was re-suspended using a Vortex-Genie® set at 2700 rpm.

A series of dilutions was required to prepare the ideal concentration for hemacytometer counts. If the OD was 10, a 1:20 dilution would be performed to achieve 0.5 OD which would give the ideal amount of cells to be counted per square, 20-30. In order to reduce inaccuracy in the dilution due to corn solids, multiple dilutions with cut 100-1000 μL BioHit pipette tips were required. Approximately, 1 cm was cut off the tips to increase the opening which prevented the tip from clogging. For a 1:20 final dilution, an initial 1:1 dilution of fermentation sample and 0.9% NaCl solution was prepared. Then, a 1:1 dilution of the previous solution (i.e., the initial 1:1 dilution) and 0.9% NaCl solution (the second dilution) was generated followed by a 1:5 dilution of the second dilution and Trypan Blue Solution. Samples were vortexed between each dilution and cut tips were rinsed into the 0.9% NaCl and Trypan Blue solutions.

The cover slip was carefully placed on top of the hemacytometer (Hausser Scientific Bright-Line 1492). An aliquot (10 μL) was drawn of the final Trypan Blue dilution with an m20 Variable Channel BioHit pipette with 2-20 μL BioHit pipette tips and injected into the hemacytometer. The hemacytometer was placed on the Zeis Axioskop 40 microscope at 40× magnification. The center quadrant was broken into 25 squares and the four corner and center squares in both chambers were then counted and recorded. After both chambers were counted, the average was taken and multiplied by the dilution factor (20), then by 25 for the number for squares in the quadrant in the hemacytometer, and then divided by 0.0001 mL which is the volume of the quadrant that was counted. The sum of this calculation is the number cells per mL.

LC Analysis of Fermentation Products in the Aqueous Phase

Samples were refrigerated until ready for processing. Samples were removed from refrigeration and allowed to reach room temperature (about one hour). Approximately 300 μL of sample was transferred with a m1000 Variable Channel BioHit pipette with 100-1000 μL BioHit pipette tips into a 0.2 um centrifuge filter (Nanosep® MF modified nylon centrifuge filter), then centrifuged using a Eppendorf, 5415C for five minutes at 14,000 rpm. Approximately 200 μL of filtered sample was transferred into a 1.8 auto sampler vial with a 250 μL glass vial insert with polymer feet. A screw cap with PTFE septa was used to cap the vial before vortexing the sample with a Vortex-Genie® set at 2700 rpm.

Sample was then run on Agilent 1200 series LC equipped with binary, isocratic pumps, vacuum degasser, heated column compartment, sampler cooling system, UV DAD detector and RI detector. The column used was an Aminex HPX-87H, 300×7.8 with a Bio-Rad Cation H refill, 30×4.6 guard column. Column temperature was 40° C., with a mobile phase of 0.01 N sulfuric acid at a flow rate of 0.6 mL/min for 40 minutes. Results are shown in Table 1.

TABLE 1 Retention times of fermentation products in aqueous phase HPLC 302/310 RID Range of UV Normalized to 10 μL Retention Standards, Retention injections FW Time, min g/L Time, min citric acid 192.12 8.025 0.3-17 7.616 glucose 180.16 8.83 0.5-71 pyruvic acid (Na) 110.04 9.388  0.1-5.2 8.5 A-Kiv (Na) 138.1 9.91 0.07-5.0  8.55 2,3-dihydroxyisovaleric 156.1 10.972  0.2-8.8 10.529 acid (Na) succinic acid 118.09 11.561 0.3-16 11.216 lactic acid (Li) 96.01 12.343 0.3-17 11.948 glycerol 92.09 12.974 0.8-39 formic acid 46.03 13.686 0.2-13 13.232 acetate (Na) 82.03 14.914 0.5-16 14.563 meso-butanediol 90.12 17.583 0.1-19 (+/−)-2,3-butanediol 90.12 18.4 0.2-19 isobutyric acid 88.11 19.685  0.1-8.0 19.277 ethanol 46.07 21.401 0.5-34 isobutyraldehyde 72.11 27.64  0.01-0.11 isobutanol 74.12 32.276 0.2-15 3-OH-2-butanone (acetoin) 88.11 0.1-11 17.151

GC Analysis of Fermentation Products in the Solvent Phase

Samples were refrigerated until ready for processing. Samples were removed from refrigeration and allowed to reach room temperature (about one hour). Approximately 150 μL of sample was transferred using a m1000 Variable Channel BioHit pipette with 100-1000 μL BioHit pipette tips into a 1.8 auto sampler vial with a 250 μL glass vial insert with polymer feet. A screw cap with PTFE septa was used to cap the vial.

Sample was then run on Agilent 7890A GC with a 7683B injector and a G2614A auto sampler. The column was a HP-InnoWax column (30 m×0.32 mm ID, 0.25 μm film). The carrier gas was helium at a flow rate of 1.5 mL/min measured at 45° C. with constant head pressure; injector split was 1:50 at 225° C.; oven temperature was 45° C. for 1.5 minutes, 45° C. to 160° C. at 10° C./min for 0 minutes, then 230° C. at 35° C./min for 14 minutes for a run time of 29 minutes. Flame ionization detection was used at 260° C. with 40 mL/min helium makeup gas. Results are shown in Table 2.

TABLE 2 Retention times of fermentation products in solvent phase GC 302/310 Solvent Range of Normalized to 10 μL Retention Standards, injections FW Time, min g/L isobutyraldehyde 72.11 2.75  0.7-10.4 ethanol 46.07 3.62 0.5-34 isobutanol 74.12 5.53 0.2-16 3-OH-2-butanone (acetoin) 88.11 8.29 0.1-11 (+/−)-2,3-butanediol 90.12 10.94 0.1-19 isobutyric acid 88.11 11.907  0.1-7.9 meso-butanediol 90.12 11.26  0.1-6.5 glycerol 92.09 16.99 0.8-9 

Samples analyzed for fatty acid butyl esters were run on Agilent 6890 GC with a 7683B injector and a G2614A auto sampler. The column was a HP-DB-FFAP column (15 meters×0.53 mm ID (Megabore), 1-micron film thickness column (30 m×0.32 mm ID, 0.25 μm film). The carrier gas was helium at a flow rate of 3.7 mL/min measured at 45° C. with constant head pressure; injector split was 1:50 at 225° C.; oven temperature was 100° C. for 2.0 minutes, 100° C. to 250° C. at 10° C./min, then 250° C. for 9 minutes for a run time of 26 minutes. Flame ionization detection was used at 300° C. with 40 mL/min helium makeup gas. The following GC standards (Nu-Chek Prep; Elysian, Minn.) were used to confirm the identity of fatty acid isobutyl ester products: iso-butyl palmitate, iso-butyl stearate, iso-butyl oleate, iso-butyl linoleate, iso-butyl linolenate, iso-butyl arachidate.

Examples 1-14 describe various fermentation conditions that may be used for the claimed methods. As an example, some fermentations were subjected to Lipase Treatment pre-liquefaction and others were subjected to Lipase Treatment post-liquefaction. In other examples, the fermentation was subjected to Heat inactivation Treatment. Following fermentation, the effective isobutanol titer (Eff Iso Titer) was measured, that is, the total grams of isobutanol produced per liter aqueous volume. Results are shown in Table 3.

The following relates to the analysis described in examples 68-71. Aqueous substrate analysis was accomplished by HPLC using a Biorad Aminex HPX-87H column in an isocratic method with 0.01N sulfuric acid as eluent on a Waters Alliance 2695 Separations Module (Milford, Mass.). Flow rate was 0.6 mL/min, column temperature 40° C., injection volume 10 μl and run time 38 min. Detection was carried out with a refractive index detector (Waters 2414 RI) operated at 40° C. and an UV detector (Waters 2996 PDA) at 210 nm.

GC/MS analysis of extractant was accomplished using an Agilent GC/MS/MS 7000B system (Agilent, Wilmington, Del.) equipped with a GERSTEL Dual Head MultiPurpose Sampler XL (Gerstel, Baltimore, Md.). Prior to injections, samples were kept at RT (25° C.) in a heated agitator. Methanol was used as wash solution. Injection volume was 1 μl. A Supelco SLB-5 ms column, 30 m×250 μm×0.25 μm was used for separation. Other device parameters were: constant helium flow at 1.5 ml/min, split ratio 1:10, inlet temperature: 300° C., transfer line: 300° C. Temperature program was: 4 min at 160° C., ramp to 235° C. at 4° C./min, hold for 10 min, ramp to 320° C. at 10° C./min, hold for either 84 min (slow method) or 24 min (fast method).

Example 1 Control

Experiment identifier 2010Y014 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 2

Experiment identifier 2010Y015 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Lipase Treatment Post-Liquefaction method, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 3

Experiment identifier 2010Y016 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Lipase Treatment Post-Liquefaction method, Nutrient Addition Prior to Inoculation method with the exception of the exclusion of ethanol, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 4

Experiment identifier 2010Y017 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Heat Kill Treatment method Post-Liquefaction, Nutrient Addition Prior to Inoculation method with the exception of the exclusion of ethanol, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 5

Experiment identifier 2010Y018 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Lipase Treatment Post-Liquefaction method with the exception of only adding 7.2 ppm lipase after liquefaction, Heat Kill Treatment method Post-Liquefaction, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 6 Control

Experiment identifier 2010Y019 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Heat Kill Treatment method Post-Liquefaction, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 7 Control

Experiment identifier 2010Y021 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Lipase Treatment Pre-Liquefaction method, Liquefaction method, the Heat Kill Treatment during liquefaction, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 8

Experiment identifier 2010Y022 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 9

Experiment identifier 2010Y023 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Lipase Treatment Post-Liquefaction method, no Heat Kill Treatment, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Corn oil fatty acids made from crude corn oil was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 10

Experiment identifier 2010Y024 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Lipase Treatment Pre-Liquefaction method, Liquefaction method, Heat Kill Treatment during liquefaction, the Nutrient Addition Prior to Inoculation method with the exception of there being no addition of ethanol, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Oleyl alcohol was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 11

Experiment identifier 2010Y029 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Lipase Treatment Pre-Liquefaction method, Liquefaction method, Heat Kill Treatment during liquefaction, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Corn oil fatty acids made from crude corn oil was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 12

Experiment identifier 2010Y030 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Lipase Treatment Pre-Liquefaction method, Liquefaction method, Heat Kill Treatment during liquefaction, Nutrient Addition Prior to Inoculation method with the exception of there being no addition of ethanol, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Corn oil fatty acids made from crude corn oil was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 13 Control

Experiment identifier 2010Y031 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Lipase Treatment Post Liquefaction method, no Heat Kill Treatment, Nutrient Addition Prior to Inoculation method with the exception of there being no addition of ethanol, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Corn oil fatty acids made from crude corn oil was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

Example 14

Experiment identifier 2010Y032 included: Seed Flask Growth method, Initial Fermentation Vessel Preparation method, Liquefaction method, Lipase Treatment Post-Liquefaction method, no Heat Kill Treatment, Nutrient Addition Prior to Inoculation method, Fermentation Vessel Inoculation method, Fermentation Vessel Operating Conditions method, and all of the Analytical methods. Corn oil fatty acids made from crude corn oil was added in a single batch between 0.1-1.0 hr after inoculation. The butanologen was NGCI-070.

TABLE 3 Fermentation conditions for Examples 1-14 Eff Iso max Eff Example Experimental Max cell Ethanol Heat Kill Titer Iso rate # Identifier Lipase Count × 10⁷ g/L Solvent Lipase g/L* g/L/h 1 2010Y014 none 27.2 5 Oleyl none 56.0 0.79 alcohol 2 2010Y015 10 ppm 31.5 5 Oleyl none 52.4 0.74 alcohol 3 2010Y016 10 ppm 6.7 0 Oleyl none 25.9 0.36 alcohol 4 2010Y017 none 7.9 0 Oleyl post - 17.2 0.25 alcohol liquefaction 5 2010Y018 7.2 ppm  16.2 5 Oleyl post - 45.8 0.66 alcohol liquefaction 6 2010Y019 none 17.5 5 Oleyl post - 48.1 0.69 alcohol liquefaction 7 2010Y021 10 ppm 21.2 5 Oleyl during 46.8 0.82 alcohol liquefaction 8 2010Y022 none 9 5 Oleyl during 56.2 0.87 alcohol liquefaction 9 2010Y023 10 ppm 12.8 5 Corn Oil none 60.3 1.3 Fatty Acids 10 2010Y024 10 ppm 25.3 0 Oleyl during 19.8 0.33 alcohol liquefaction 11 2010Y029 10 ppm 21.2 5 Corn Oil during 28.36 0.52 Fatty liquefaction Acids 12 2010Y030 10 ppm 9 0 Corn Oil during 12.71 0.24 Fatty liquefaction Acids 13 2010Y031 10 ppm 12.8 0 Corn Oil none 18.86 0.35 Fatty Acids 14 2010Y032 10 ppm 25.3 5 Corn Oil none 53.36 0.92 Fatty Acids *The “Eff Iso Titer g/L” = total grams of isobutanol produced per liter aqueous volume

Examples 15 and 16 represent a comparison of fermentation and isobutanol production in the presence and absence of post-liquefaction lipase treatment. Results are shown in Tables 4 and 5.

Example 15

Experiment identifier 2010Y026 included: Seed Flask Growth method, Initial Fermentation vessel Preparation method, the Liquefaction method, the Lipase Treatment Post-Liquefaction method, the Nutrient Addition Prior to Inoculation method, Fermentation vessel Inoculation method, Fermentation vessel Operating Conditions method, and all of the Analytical methods. Corn oil fatty acids made from crude corn oil was added in a single batch between 0.1-1.0 hr after inoculation. The corn oil fatty acids extracting solvent was added in equal volume to the broth volume. The butanologen was PNY2205. Between 46 hrs and 61 hrs fermentation time, the addition of 274 g of a 50% w/w sterile, glucose solution was made because the glucose made from corn mash had been all but depleted.

Example 16

Experiment identifier 2010Y027 included: Seed Flask Growth method, Initial Fermentation vessel Preparation method, the Liquefaction method, the Nutrient Addition Prior to Inoculation method, Fermentation vessel Inoculation method, Fermentation vessel Operating Conditions method, and all of the Analytical methods. HD OCENOL® 90/95 (oleyl alcohol, CAS No. 143-28-2, Cognis, Monheim, Del.) was added in a single batch between 0.1-1.0 hr after inoculation. The oleyl alcohol extracting solvent was added in equal volume to the broth volume. The butanologen was PNY2205.

TABLE 4 Glucose Biomass Experimental Lipase Extracting Consumed produced ID Addition Solvent (g) (cfu/mL) 2010Y026 Yes corn oil fatty acids 326.3 34.2 × 10⁷ 2010Y027 No oleyl alcohol 234.9 33.0 × 10⁷

TABLE 5 Maximum Effec- Maximum residual tive effective i- Lipase i-BuOH in i-BuOH BuOH production Yield Addi- aqueous titer rate g/L/hr g i-BuOH/ Exp. ID tion (g/L) (g/L) (aqueous volume) g glucose 2010Y026 Yes 4.7 72.2 1.41 0.26 2010Y026 No 10.0 55.4 1.19 0.25

Examples 17 to 22 represent a comparison of the effect of fresh extractant versus recycled extractant on fermentation and isobutanol production. Results are shown in Table 6. For these examples, 2 L and 10 L fermentations were prepared as described below.

10 L Pre-Seed Flask Growth

A Saccharomyces cerevisiae strain (strain PNY2242 described above) that was engineered to produce isobutanol from a carbohydrate source, with pdc1 deleted, pdc5 deleted, and pdc6, deleted was grown to 0.6-0.7 g/L dcw (OD₆₀₀ 1.5-2.5—Thermo Helios α Thermo Fisher Scientific Inc., Waltham, Mass.) in seed flasks (10 mL synthetic medium in a 125 mL, vented flask) from a frozen culture. The culture was grown at 29-31° C. in an incubator rotating at 260 rpm. The frozen culture was previously stored at −80° C. The composition synthetic seed flask medium was:

-   -   10.0 g/L dextrose     -   3.5 mL/L ethanol, anhydrous     -   3.7 g/L ForMedium™ Synthetic Complete Amino Acid (Kaiser)         Drop-Out: without HIS, without URA (Reference No. DSCK162CK)     -   6.7 g/L Difco Yeast Nitrogen Base without amino acids (No.         291920)     -   1% Ergersterol in 1:1::Tween 80:Ethanol

Two milliliters from the first seed flask culture was transferred to 25 mL in a 250 mL, vented flask and grown at 29-31° C. in an incubator rotating at 260 rpm. The second seed flask uses the same synthetic medium as used above.

The culture was grown to 0.6-0.7 g/L dcw (OD₆₀₀ 1.0-3.0). Then, 8 mL of this second flask culture was added to three flasks (2 L, vented, baffled flasks) with 200 mL of synthetic medium. The culture was grown in an incubator at 29-31° C. for 18-24 hrs. The three seed flasks use the same synthetic medium as used in the first two seed flasks. These three flasks (600 mL of flask broth) are used to inoculate the propagation tank at a final aqueous volume of 6 L.

10 L Propagation Tank Liquefaction

A 10 L, B. Braun BioStat C fermentor was prepared for use. An inline pH probe was placed in the fermentor. The zero was calibrated at pH=7. The span was calibrated at pH=4. The probe was then placed into the fermentation vessel, through a side port. A dissolved oxygen probe (pO₂ probe) was also placed into the fermentor through a side port. Tubing used for delivering nutrients, seed culture, extracting solvent, and base were attached to the head plate and the ends were foiled. The valve for harvesting and sampling were sterilized with low pressure steam and a steam trap at >121° C. for >20 minutes.

The fermentation vessel temperature was controlled at 30° C. with a thermocouple and house water circulation loop. Wet corn kernels (#2 yellow dent) were ground using a hammer mill with a 1.0 mm screen, and the resulting ground whole corn kernels were then added to the fermentation vessel at a charge that was 10-20% (dry corn solids weight) of the liquefaction reaction mass. Difco Yeast Extract was added to the fermentor at 0.5% w/w of the total batch weight.

An alpha-amylase was added to the fermentation vessel per its specification sheet while the fermentation vessel was mixing at 300-1500 rpm, with sterile, house N₂ being added at 1-2 slpm through the sparger. The temperature set-point was changed from 55° C. to 95° C. in 5° C. step changes with a 5-15 minute hold at each step to ensure good mixing. When the temperature was >90° C., the liquefaction cook time was started and the liquefaction cycle was held at >90° C. for 60 minutes. The fermentation vessel temperature set-point was set to the fermentation temperature of 30° C. after the liquefaction cycle was complete. N₂ was redirected from the sparger to the head space to prevent foaming without the addition of a chemical antifoaming agent.

10 L Propagation Tank Operation

The fermentation vessels pO₂ probe was calibrated to zero while N₂ was being added to the fermentation vessel. The fermentation vessels pO₂ probe was calibrated to its span with sterile air sparging at 400 rpm. The fermentation vessel was inoculated from the final stage of the Pre-Seed Flask Growth step. The three shake flasks were removed from the incubator/shaker and added to a sterile vessel. The content of the sterile vessel was added to 5.3-5.5 L of the liquefied mash that was made during the Propagation Tank Liquefaction method.

The fermentation temperature was controlled between 29-31° C. The agitation speed was fixed at 400 rpm. Air was sparged for the entire fermentation at 2.0 slpm. The pH was controlled at 5.4-5.5 by using NH₄OH and the PID control loop for the fermentor. There was 0.3-0.5 bar of back pressure set on the fermentor, controlled by a PID loop that controlled a back pressure control valve.

At 16-20 hrs after inoculation, a glucoamylase (1.8 mL of Distillase® L-400, Genencor, Palo Alto, Calif.) was added to start simultaneous saccharification and fermentation, releasing glucose from the dissolved starch. Also, 5.5 L of HD OCENOL® 90/95 (oleyl alcohol, Cognis, Monheim, Del.) was added to the fermentor. At 34-36 hrs, the agitator speed was reduced to 100 rpm. After 10 minutes, the agitator was turned off and the airflow to the fermentor was changed from sparge mode to overlay mode.

10 L Production Tank Liquefaction

A 10 L Production Tank Liquefaction was performed as described above. The fermentation vessel temperature was controlled at 30° C. with a thermocouple and house water circulation loop. Wet corn kernels (#2 yellow dent) were ground using a hammer mill with a 1.0 mm screen, and the resulting ground whole corn kernels were then added to the fermentation vessel at a charge that was 25-35% (dry corn solids weight) of the liquefaction reaction mass. A 75 mL addition of a 100× Vitamin Solution (2 g/L thiamine and 10 g/L nicotinic acid) was made to the fermentor. An alpha-amylase was added to the fermentation vessel was added as described above. Also, an addition of 6-7 mL/L anhydrous ethanol was made to the fermentor after the fermentor was returned to 30° C.

10 L Production Tank Operation

The fermentation vessels pO₂ probe was calibrated to zero while N₂ was being added to the fermentation vessel. The fermentation vessels pO₂ probe was calibrated to its span with sterile air sparging at 400 rpm. The fermentation vessel was inoculated from Propagation Tank. An aseptic transfer was made from the Propagation Tank after 36 hrs of growth time in the propagation tank and the fermentation agitation was turned off for >10 minutes. This allowed for significant separation of the oleyl alcohol and the aqueous phase. The aseptic transfer was made from the harvest valve on the Propagation Tank, which is located at the bottom of this fermentor. Approximately 10% v/v was added to the Production Tank, based on the tanks final non-solvent volume after transfer.

The fermentation temperature was controlled between 29-31° C. The agitation speed was fixed at 400 rpm. Air was sparged for the entire fermentation at 2.0 slpm. The pH was controlled at 5.2-5.3 by using NH₄OH and the PID control loop for the fermentor. There was 0.3-0.5 bar of back pressure set on the fermentor, controlled by a PID loop that controlled a back pressure control valve.

Just prior to inoculation, 25-35% v/v Cognis Emery® 610 SOYA Fatty Acid was aseptically added to the fermentor. The fermentor was inoculated with 10% v/v fermentation broth after the completion of the 10 L Propagation Tank Operation method.

Just after inoculation, a glucoamylase (Distillase® L-400) was added to release glucose from the starch. Additional glucoamylase additions were made when needed to maintain the glucose excess. Just after inoculation, a lipase (Novozymes Lipolase® 100L) was added to the fermentor at 4-15 ppm.

2 L Pre-Seed Flask Growth

A 2 L pre-seed flask growth was prepared using a Saccharomyces cerevisiae strain (strain PNY2242 described above) and was grown to 0.6-0.7 g/L dcw (OD₆₀₀ 1.5-2.5—Thermo Helios α Thermo Fisher Scientific Inc., Waltham, Mass.) in seed flasks (10 mL synthetic medium in a 125 mL, vented flask) from a frozen culture. The culture was grown at 29-31° C. in an incubator rotating at 260 rpm. The frozen culture was previously stored at −80° C. The composition synthetic seed flask medium was:

-   -   10.0 g/L dextrose     -   3.5 mL/L ethanol, anhydrous     -   3.7 g/L ForMedium Synthetic Complete Amino Acid (Kaiser)         Drop-Out: without HIS, without URA (Reference No. DSCK162CK)     -   6.7 g/L Difco Yeast Nitrogen Base without amino acids         (No. 291920) 1% Ergersterol in 1:1::Tween 80:Ethanol.

Two milliliters from the first seed flask culture was transferred to 25 mL in a 250 mL, vented flask and grown at 29-31° C. in an incubator rotating at 260 rpm. The second seed flask uses the same synthetic medium as used above.

The culture was grown to 0.6-0.7 g/L dcw (OD₆₀₀ 1.0-3.0). Then 4 mL of this second flask culture was added to 100 mL of corn mash centrate in a 2 L flask. The culture was grown in an incubator at 29-31° C. for 18-24 hrs. Then 500 mL of HD OCENOL® 90/95 (oleyl alcohol, Cognis, Monheim, Del.) was added to the flask. The flask was allowed to grow for 6-8 hrs. Then 2 mL of a 1.2 g Distillase® L-400, (Genencor, Palo Alto, Calif.) in 80 mL of deionized water was added to the centrate to release glucose from the dissolved starch in the centrate. The culture continued to grow for 18-24 hrs. The final biomass concentration was 6-12 g/L dcw.

The corn mash centrate was made by liquefying corn in the following recipe:

1150 g tap water

340.5 g 1 mm screened ground corn

13.5 g yeast extract (Difco No. 9102333, low dusting)

27 g peptone

4.1 g urea

40.5 mg nicotinic acid

40.5 mg thiamine.

Then the material was centrifuged for 30 minutes in a Sorval RC5C centrifuge. The supernatant was separated from the solids pellet. The supernatant was heated in a Steris autoclave for a 5 minute liquid cycle and is defined as centrate.

2 L Fermentation Preparation

2 L Initial Fermentation Vessel Preparation

A 2 L Initial Fermentation Vessel Preparation was prepared as described above. The fermentation vessel temperature was controlled at 55° C. with a thermocouple and house water circulation loop. Wet corn kernels (#2 yellow dent) were ground using a hammer mill with a 1.0 mm screen, and the resulting ground whole corn kernels were then added to the fermentation vessel at a charge that was 25-30% (dry corn solids weight) of the liquefaction reaction mass. In addition, Liquefaction was conducted as described above. An alpha-amylase was added to the fermentation vessel per its specification sheet while the fermentation vessel was mixing at 300-1200 rpm, with sterile, house N₂ being added at 0.3 slpm through the sparger.

2 L Additions Prior to Inoculation

The following nutrients were added to the fermentation vessel prior to inoculation, after liquefaction, on a post-inoculation volume basis:

30 mg/L of nicotinic acid

30 mg/L of thiamine

1 mL/L of a 1% ergersterol w/v solution in 1:1:Tween 80:Ethanol

6.3 mL/L ethanol

2 g/L urea.

2 L Fermentation Vessel Inoculation

The fermentation vessels pO₂ probe was calibrated to zero while N₂ was being added to the fermentation vessel. The fermentation vessels pO₂ probe was calibrated to its span with sterile air sparging at 300 rpm. The fermentation vessel was inoculated from the final stage of the Pre-Seed Flask Growth step. The shake flask was removed from the incubator/shaker and centrifuged for 30 minutes. The liquid (oleyl alcohol and aqueous supernatant) was discarded and the cell pellet was re-suspended in the Pre-Seed Flask Growth medium (synthetic medium). The 100 mL of the aqueous phase was transferred to a sterile inoculation bottle. The inoculum was pumped into the fermentation vessel through a peristaltic pump.

2 L Lipase Addition After Inoculation

A Lipolase® solution (100 L stock solution) was prepared to an enzyme concentration of 1.2-1.4 mg/mL. The solution was added to the fermentation after inoculating the fermentor to the desired part per million concentration based on the non-solvent volume. The addition time occurred <1 hr after inoculating the fermentor.

2 L Soy Bean Oil Fatty Acid Addition

To the fermentation vessel was added 0.1-0.5 L/L (post-inoculation volume) of either virgin Cognis Emery® 610 SOYA Fatty Acid or recycled Cognis Emery® 610 SOYA Fatty Acids that contains 0-30 weight percent fatty acid butyl ester.

2 L Fermentation Vessel Operating Conditions

The fermentation vessel was operated at 30° C. for the entire growth and production stages. The pH was allowed to drop from a pH between 5.7-5.9 to a control set-point of 5.25 without adding any acid. The pH was controlled for the remainder of the growth and production stage at a pH=5.2 with ammonium hydroxide. Sterile air was added to the fermentation vessel, through the sparger, at 0.2-0.3 slpm for the remainder of the growth and production stages. The pO₂ was not controlled. The agitator was set to a fixed rpm at 300 rpm. The stir shaft had two Rushton impellers below the aqueous level and one pitched blade impeller above the aqueous level. The glucose was supplied through simultaneous saccharification and fermentation of the liquified corn mash by adding a glucoamylase. The glucose was kept excess (1-50 g/L) for as long as starch was available for saccharification.

A 5-20 mL sample was pulled from a fermentation vessel and placed in a centrifuge tube and centrifuged for cell mass measurement using the procedure described above. In addition, Analytical methods such as gas analyses as well as LC analyses of fermentation products in the aqueous phase and GC analyses of fermentation products in the solvent phase were conducted as described above.

The fermentation conditions for Examples 17 to 22 are provided below and a summary of the results (virgin soy bean oil fatty acids and recycled soy bean fatty acids with fatty acid butyl esters) are shown in Table 6.

Example 17

Experimental Identifier GLNOR1050 included: 10 L Pre-Seed Flask Growth, 10 L Propagation Tank Liquefaction, 10 L Propagation Tank Operation, 10 L Production Tank Liquefaction, 10 L Production Tank Operation with 10 ppm Lipolase® 100L (Genencor) added to the fermentor, extractant: Virgin Cognis Emery® 610 SOYA Fatty Acid (virgin soy bean oil fatty acid). The liquid solvent and non-solvent material was separated in a Sorval RC-12 centrifuge, and all Analytical methods.

Example 18

Experimental Identifier GLNOR1051 included: 10 L Pre-Seed Flask Growth, 10 L Propagation Tank Liquefaction, 10 L Propagation Tank Operation, 10 L Production Tank Liquefaction, 10 L Production Tank Operation with 4 ppm Lipolase® 100L (Genencor) added to the fermentor, extractant: Virgin Cognis Emery® 610 SOYA Fatty Acid (virgin soy bean oil fatty acid). The liquid solvent and non-solvent material was separated in a Sorval RC-12 centrifuge, and all Analytical methods.

Example 19

Identifier 2011Y029 included: 2 L Pre-Seed Flask Growth, 2 L Fermentation Preparation, 2 L Liquefaction, 2 L Additions Prior to Inoculation, 2 L Fermentation Vessel Inoculation, 2 L Lipase Addition After Inoculation at a final concentration of 10 ppm, 2 L Recycled Soy Bean Oil Fatty Acid Addition (Recycled Cognis Emery® 610 SOYA Fatty Acid and fatty acid butyl ester from Example 56A—50% v/v solvent load), 2 L Fermentation Vessel Operating Conditions, and all Analytical methods.

Example 20

Identifier 2011Y030 included: 2 L Pre-Seed Flask Growth, 2 L Fermentation Preparation, 2 L Liquefaction, 2 L Additions Prior to Inoculation, 2 L Fermentation Vessel Inoculation, 2 L Lipase Addition After Inoculation at a final concentration of 10 ppm, added 0.4 L/L (post-inoculation volume) Virgin Cognis Emery® 610 SOYA Fatty Acids that included 20-30% fatty acid butyl esters, 2 L Fermentation Vessel Operating Conditions, and all Analytical methods.

Example 21

Identifier 2011Y031 included: 2 L Pre-Seed Flask Growth, 2 L Fermentation Preparation, 2 L Liquefaction, 2 L Additions Prior to Inoculation, 2 L Fermentation Vessel Inoculation, 2 L Lipase Addition After Inoculation at a final concentration of 10 ppm, 2 L Recycled Soy Bean Oil Fatty Acid Addition (Recycled Cognis Emery® 610 SOYA Fatty Acid and fatty acid butyl ester from Example 56B—10% v/v solvent load), 2 L Fermentation Vessel Operating Conditions, and all Analytical methods.

Example 22

Identifier 2011Y032 included: 2 L Pre-Seed Flask Growth, 2 L Fermentation Preparation, 2 L Liquefaction, 2 L Additions Prior to Inoculation, 2 L Fermentation Vessel Inoculation, 2 L Lipase Addition After Inoculation at a final concentration of 10 ppm, added 0.4 L/L (post-inoculation volume) Virgin Cognis Emery® 610 SOYA Fatty Acids, 2 L Fermentation Vessel Operating Conditions, and all Analytical methods.

TABLE 6 Solvent Max i- EOR Lipase Max Cell Loading BuOH (aq) Volumetric Exp. ID ppm Count × 10⁷ Vol % g/L Rate g/L/hr Extractant GLNOR 10 21.3 28% 6.9 0.97 Virgin Soy Bean Oil 1050 Fatty Acid GLNOR 4 20.9 28% 8.9 0.83 Virgin Soy Bean Oil 1051 Fatty Acid 2011Y029 10 20.9 50% 8.2 0.85 Recycled Soy Bean Oil Fatty Acid and Fatty Acid Butyl Ester 2011Y030 10 24.4 40% 9.8 0.88 Virgin Soy Bean Oil Fatty Acid and Fatty Acid Butyl Ester 2011Y031 10 9.8 10% 12.7 0.42 Recycled Soy Bean Oil Fatty Acid and Fatty Acid Butyl Ester 2011Y032 10 26.5 40% 6.8 0.94 Virgin Soy Bean Oil Fatty Acid

Example 23

The following example describes the production of isobutanol by fermentation using sucrose as a fermentable carbon source.

Generation of Biomass

Inoculum: A seed medium was prepared to initiate the growth of the isobutanologen. The composition of the seed medium was as follows: ammonium sulfate, 5 g/L; potassium phosphate monobasic, 3 g/L; magnesium sulfate heptahydrate, 0.5 g/L; ethanol, 3.2 g/L; yeast extract (BBL), 5 g/L; glucose, 10 g/L; MES buffer, 150 mmol/L; biotin, 50 μg/L; and a trace element solution, 1 mL/L, which contains in 1 L water, 15 g EDTA, 4.5 g zinc sulfate heptahydrate, 0.8 g manganese chloride dehydrate, 0.3 g cobalt chloride hexahydrate, 0.3 g copper sulfate pentahydrate, 0.4 g disodium molybdenum dehydrate, 4.5 g calcium chloride dihydrate, 3 g iron sulfate heptahydrate, 1 g boric acid, 0.1 g potassium iodide. The pH was adjusted to 5.5, and then the medium filter sterilized through an 0.22 p sterile filter apparatus.

Preparation of the 10 L Fermentor for Biomass Production

A single vial of the isobutanologen PNY2205 was aseptically transferred to 15 mL seed medium in a 125 mL vented flask for over night growth at 30° C. and 260 rpm shaking. The culture was aseptically transferred to 500 mL of the same medium in a 2 L baffled, vented flask for over night growth at 30° C. and 260 rpm shaking, and transferred to a prepared 10 L Sartorius C fermentor (Sartorius AG, Goettingen, Germany) when the culture reached OD₆₀₀ 7.

A 10 L Sartorius C fermentor was prepared with 6 L initial volume of growth medium. The growth medium composition and preparation was as follows: prior to sterilization, ammonium sulfate, 1 g/L; potassium phosphate monobasic, 5 g/L; magnesium sulfate, heptahydrate, 2 g/L; yeast extract (Amberex™ 695), 2 g/L; Antifoam Sigma 204, 0.5 mL/L; biotin, 100 μg/L; and 1 mL/L trace element solution (prepared in 1 L water: 15 g EDTA, 4.5 g zinc sulfate heptahydrate, 0.8 g manganese chloride dehydrate, 0.3 g cobalt chloride hexahydrate, 0.3 g copper sulfate pentahydrate, 0.4 g disodium molybdenum dehydrate, 4.5 g calcium chloride dihydrate, 3 g iron sulfate heptahydrate, 1 g boric acid, 0.1 g potassium iodide). After steam sterilization at 121° C. in place, the vessel was cooled, and 60 g of the feed medium was added. The feed medium was prepared as follows: sucrose, 50% solution, 2.97 L; biotin, 1.4 mg; 34 mL of the trace mineral solution; titrated to pH 7.5 with 5N sodium hydroxide and steam sterilized; post sterilization and cooling, 130 mL ethanol and 320 mL of a 20% (w/v) filter sterilized solution of yeast extract (Amberex™ 695) was added. The initial sugar concentration in the 10 L fermentor was thus 3.7 g/L sucrose, 0.8 g/L glucose, and 0.8 g/L fructose.

The fermentation was controlled at pH 5.5 (with ammonium hydroxide addition), 30° C., airflow at 2.0 standard liters per minute, dissolved oxygen at 30% by agitation control, and 0.5 barg back pressure. After inoculation, the sugar was consumed until the residual measurement of glucose was less than 0.1 g/L, and then the feed program began; this occurred at 11 hours elapsed fermentation time. The program was established to maintain sucrose limitation until OD₆₀₀ of 20 (approximately 8 g/L dry cell weight) was achieved, with a programmed growth rate of 0.1/hr. The actual measured growth rate in this experiment was 0.18/hr. The targeted OD₆₀₀ was reached after 20 hours fermentation time.

Once the target was achieved, the culture was harvested aseptically, and centrifuged in a Sorvall RC12BP centrifuge. The resulting pellet was resuspended to a final volume of 300 mL with isobutanol production medium, described below. This culture was used as the inoculum for the isobutanol production fermentors.

Isobutanol Production

Preparation of production fermentors: Two one liter glass Applikon (Applikon, Inc, Holland) fermentors associated with a Sartorius BioStat B Plus Twin control unit (Sartorius AG, Goettingen, Germany) were used for the isobutanol production. The fermentors were prepared with 1 L deionized water, and sterilized by autoclaving at 121° C. for 30 minutes. Once the fermentors cooled, the water was aseptically removed, and the volume of filter sterilized production medium, as indicated in Table 7, was added. The production medium composition was as follows: yeast nitrogen base without amino acids (Difco), 6.7 g/L; Yeast Synthetic Drop-out Medium Supplements without histidine, leucine, tryptophan, and uracil (Sigma), 2.70 g/L; tryptophan, 1.6 mg/L; leucine, 8 mg/L; ethanol, 2.8 g/L; Antifoam Sigma 204, 0.2 mL/L; sucrose, 25 g/L. Just before inoculation, filter sterilized lipase solution was as indicated in Table 7. The lipase solution was prepared by dilution of Lipolase® L100 (Sigma) in 10 mM potassium phosphate buffer, pH 7, to a final concentration of 1.25 mg protein/mL. The solution was prepared and stored for one day at 5° C. before addition to the fermentors.

TABLE 7 Fermentation Broth SOFA lipase Fermentor (mL) (mL) (mg/L) A 440 320 0 B 440 320 10 C 520 240 10 D 520 240 25

The fermentors were controlled at pH 5.2 (by addition of 20% potassium hydroxide), 30° C., airflow at 0.2 standard liters per minute, and dissolved oxygen at 3% by agitation control.

The fermentors were each inoculated with 40 mL of the concentrated biomass, to initial OD₆₀₀ 20-25 (approximately 8-10 g/L dry cell weight). An addition 4 mL of a filter sterilized vitamin solution (thiamine-HCl, 1 mg/mL; nicotinic acid, 1 mg/mL, in water) was added at inoculation, as was the volume of filter sterilized Soya Oil Fatty Acids (SOFA) indicated in Table 7. Samples (5-10 mL) were drawn every 2-3 hours, and assayed for glucose and sucrose by a YSI Select Biochemistry Analyzer (YSI, Inc., Yellow Springs, Ohio). As sucrose was consumed, a feed of 50% sucrose (w/w) was added to maintain a concentration of 5-30 g/L. The aqueous and organic phases of the samples were separated and analyzed by the HPLC method described above via an Agilent 1100 HPLC. For analysis of organic acids and alcohols, a Shodex® Sugar SH1011 column was used with 0.01 N sulfuric acid mobile phase. For analysis of sucrose, glucose, and fructose, a BioRad Aminex® HPX-87N column with 0.01 M Na₂HPO₄ (pH 8) mobile phase was used.

Each of the fermentors with lipase added had lower concentrations of isobutanol in the aqueous phase and free isobutanol in the solvent phase. The aqueous and solvent phase concentrations of isobutanol are shown in FIG. 6. Addition of more lipase at the same solvent loading also resulted in lower aqueous titers of isobutanol and lower free isobutanol in the solvent, and more isobutanol as FABE.

The cultivations which included lipase resulted in a higher effective titer of isobutanol than the control fermentor without lipase. FIG. 7 shows the effective titer of isobutanol. In this example, the effective titer was calculated based on the initial measured weight of broth in the fermentor after inoculation and the initial measured weight of solvent charged to the fermentor. The solvent density was assumed to be 0.88 g/mL and the aqueous broth density 1.00 g/mL throughout the fermentation. Addition of more lipase at the lower solvent loading did result in higher effective titers of isobutanol (D vs C), but not as much as increasing the relative volume of solvent (C vs B).

Sugar consumed, calculated in glucose equivalents, was higher in fermentors with lipase added, shown in FIG. 8. Glucose equivalents consumed is calculated from the measured sugars fed and remaining in the fermentor, with each mole of sucrose counted as two moles of glucose and each mole of fructose counted as one mole of glucose, then converted to grams via the molecular weight of glucose. The concentration of glucose equivalents consumed is also calculated on the basis of the initial volume of fermentation broth after inoculation.

Example 24 Lipase Treatment of Liquefied Corn Mash for Simultaneous Saccharification and Fermentation with In-situ Product Removal Using Oleyl Alcohol

Samples of broth and oleyl alcohol taken from fermentations run as described above in Examples 1, 2, and 3 were analyzed for wt % lipid (derivatized as fatty acid methyl esters, FAME) and for wt % free fatty acid (FFA, derivatized as fatty acid methyl esters, FAME) according to the method described by E. G. Bligh and W. J. Dyer (Canadian Journal of Biochemistry and Physiology, 37:911-17, 1959, hereafter Reference 1). The liquefied corn mash that was prepared for each of the three fermentations was also analyzed for wt % lipid and for wt % FFA after treatment with Lipolase® 100 L (Novozymes) (10 ppm of Lipolase® total soluble protein (BCA protein analysis, Sigma Aldrich)) per kg of liquefaction reaction mass containing 30 wt % ground corn kernels). No lipase was added to the liquefied corn mash in Example 1 (control), and the fermentations described in Examples 2 and 3 containing liquefied corn mash treated with lipase (no heat inactivation of lipase) were identical except that no ethanol was added to the fermentation described in Example 3.

The % FFA in lipase-treated liquefied corn mash prepared for fermentations run as described in Examples 2 and 3 was 88% and 89%, respectively, compared to 31 without lipase treatment (Example 1). At 70 h (end of run (EOR)), the concentration of FFA in the OA phase of fermentations run as described in Examples 2 and 3 (containing active lipase) was 14% and 20%, respectively, and the corresponding increase in lipids (measured as corn oil fatty acid methyl ester derivatives) was determined by GC/MS to be due to the lipase-catalyzed esterification of COFA by OA, where COFA was first produced by lipase-catalyzed hydrolysis of corn oil in the liquefied corn mash; the production of oleyl palmitate, oleyl stearate, and oleyl oleate was confirmed by GC/MS, and a fourth ester was tentatively identified as oleyl linoleate. Results for FFA and lipid analysis are shown in Table 8.

TABLE 8 Lipid and free fatty acid content of fermentations containing oleyl alcohol as ISPR extractant and active lipase time (h), lipids FFA lipids FFA lipids + fermentation lipase sample (wt %) (wt %) (g) (g) FFA (g) % FFA Example 1 none liq. mash 0.61 0.28 5.3 2.4 7.7 31 Example 1 none 0.8 h, broth 0.49 0.22 5.5 2.5 8.0 31 Example 1 none 31 h, broth 0.19 0.03 2.1 0.3 2.4 13 Example 1 none 31 h, OA 0.36 0.21 3.4 2.0 5.3 37 Example 1 none 70 h, broth 0.15 0.03 1.7 0.3 2.0 15 Example 1 none 70 h, OA 0.57 0.25 5.3 2.3 7.7 31 Example 2 10 ppm liq. mash 0.13 0.97 1.1 8.5 9.6 88 Example 2 10 ppm 0.8 h, broth 0.15 0.62 1.7 7.0 8.7 81 Example 2 10 ppm 31 h, broth 0.16 0.05 1.8 0.5 2.3 23 Example 2 10 ppm 31 h, OA 0.37 0.23 3.5 2.2 5.7 38 Example 2 10 ppm 70 h, broth 0.17 0.02 1.9 0.3 2.2 13 Example 2 10 ppm 70 h, OA 0.60 0.10 5.7 1.0 6.7 14 Example 3 10 ppm liq. mash 0.12 0.97 1.0 8.5 9.5 89 Example 3 10 ppm 0.8 h, broth 0.32 0.40 3.6 4.5 8.1 56 Example 3 10 ppm 31 h, broth 0.17 0.05 1.9 0.6 2.5 24 Example 3 10 ppm 31 h, OA 0.38 0.22 3.6 2.1 5.7 37 Example 3 10 ppm 70 h, broth 0.15 0.02 1.7 0.2 1.9 13 Example 3 10 ppm 70 h, OA 0.46 0.12 4.4 1.1 5.6 20

Example 25 Heat Inactivation of Lipase in Lipase-treated Liquefied Corn Mash to Limit Production of Oleyl Alcohol Esters of Corn Oil Free Fatty Acids

Tap water (918.4 g) was added to a jacketed 2-L resin kettle, then 474.6 g wet weight (417.6 g dry weight) of ground whole corn kernels (1.0 mm screen on hammer mill) was added with stirring. The mixture was heated to 55° C. with stirring at 300 rpm, and the pH adjusted to 5.8 with 2 N sulfuric acid. To the mixture was added 14.0 g of an aqueous solution containing 0.672 g of Spezyme®-FRED L (Genencor®, Palo Alto, Calif.), and the temperature of the mixture increased to 85° C. with stirring at 600 rpm and pH 5.8. After 120 minutes at 85° C., the mixture was cooled to 50° C. and 45.0 mL aliquots of the resulting liquefied corn mash were transferred to 50-mL polypropylene centrifuge tubes and stored frozen at −80° C.

In a first reaction, 50 g of liquefied corn mash prepared as described above was mixed with 10 ppm Lipolase® 100 L (Novozymes) for 6 h at 55° C. and with no inactivation of lipase at 85° C. for 1 h, the mixture was cooled to 30° C. In a second reaction, 50 g of liquefied corn mash was mixed with 10 ppm Lipolase® for 6 h at 55° C., then heated to 85° C. for 1 h (lipase inactivation), then cooled to 30° C. In a third reaction, 50 g of liquefied corn mash without added lipase was mixed for 6 h at 55° C., and with no heating at 85° C. for 1 h, the mixture was cooled to 30° C., 38 g of oleyl alcohol was added, and the resulting mixture stirred for 73 h at 30° C. In a fourth reaction, 50 g of liquefied corn mash without added lipase was mixed for 6 h at 55° C., then heated to 85° C. for 1 h, then cooled to 30° C. Each of the four reaction mixtures was sampled at 6 h, then 38 g of oleyl alcohol added, and the resulting mixtures stirred at 30° C. and sampled at 25 h and 73 h. Samples (both liquefied mash and oleyl alcohol (OA)) were analyzed for wt % lipid (derivatized as fatty acid methyl esters, FAME) and for wt % free fatty acid (FFA, derivatized as fatty acid methyl esters, FAME) according to the method described by Reference 1.

The % FFA in the OA phase of the second reaction run with heat inactivation of lipase prior to OA addition was 99% at 25 h and 95% at 73 h, compared to only 40% FFA and 21% FFA at 25 h and 73 h, respectively, when the lipase in lipase-treated liquefied corn mash was not heat inactivated (first reaction). No significant change in FFA was observed in the two control reactions without added lipase. Results are shown in Table 9.

TABLE 9 Lipid and free fatty acid content of a mixture of liquefied corn mash and oleyl alcohol in the presence or absence of active or heat-inactivated lipase reaction time (h), lipids FFA lipids FFA lipid + FFA conditions sample (wt %) (wt %) (mg) (mg) (mg) % FFA 10 ppm active lipase, 6 h, liq. mash 0.08 0.71 41 345 386 89 no 85° C. heat treatment 25 h, liq. mash 0.22 0.06 105 27 132 20 25 h, OA 0.58 0.39 212 143 355 40 73 h, liq. mash 0.25 0.05 121 22 143 18 73 h, OA 0.91 0.24 333 88 420 21 10 ppm inactive lipase, 6 h, liq. mash 0.06 0.45 28 224 252 89 85° C. heat treatment 25 h, liq. mash 0.10 0.11 49 54 103 53 25 h, OA 0.02 0.96 8 366 374 99 73 h, liq. mash 0.24 0.15 117 72 189 62 73 h, OA 0.06 1.11 23 424 447 95 no lipase, 6 h, liq. mash 0.80 0.40 401 199 599 33 no 85° C. heat treatment 25 h, liq. mash 0.30 0.05 147 25 173 15 25 h, OA 0.55 0.36 212 139 351 40 73 h, liq. mash 0.23 0.05 117 26 143 23 73 h, OA 0.79 0.42 305 162 467 34 no lipase, 6 h, liq. mash 0.74 0.36 370 183 553 33 85° C. heat treatment 25 h, liq. mash 0.31 0.05 156 27 183 15 25 h, OA 0.60 0.35 233 136 369 37 73 h, liq. mash 0.20 0.05 99 23 121 23 73 h, OA 0.84 0.41 326 159 486 33

Example 26 Heat Inactivation of Lipase in Lipase-Treated Liquefied Corn Mash for Simultaneous Saccharification and Fermentation with In-Situ Product Removal Using Oleyl Alcohol

Three fermentations were run as described above in Examples 4, 5, and 6. No lipase was added to the liquefied corn mash in Examples 4 and 6 prior to fermentation, and the Lipase Treatment of the liquefied corn mash in the fermentation described in Example 5 (using 7.2 ppm of Lipolase® total soluble protein) was followed immediately by Heat Inactivation Treatment (to completely inactivate the lipase), and subsequently followed by Nutrient Addition Prior to Inoculation and fermentation. The % FFA in liquefied corn mash prepared without lipase treatment for fermentations run as described in Examples 4 and 6 was 31% and 34%, respectively, compared to 89% with lipase treatment (Example 5). Over the course of the fermentations listed in Table 10, the concentration of FFA in the OA phase did not decrease in any of the three fermentations, including that containing heat-inactivated lipase. The % FFA in the OA phase of the fermentation run according to Example 5 (with heat inactivation of lipase prior to fermentation) was 95% at 70 h (end of run (EOR)), compared to only 33% FFA for the remaining two fermentations (Examples 4 and 6) where liquefied corn mash was not treated with lipase. Results are shown in Table 10.

TABLE 10 Lipid and free fatty acid content of fermentations containing oleyl alcohol as ISPR extractant and heat-inactivated lipase (after lipase treatment of liquefied mash) time (h), lipids FFA lipids FFA lipid + fermentation lipase sample (wt %) (wt %) (g) (g) FFA (g) % FFA Example 4 none liquefied mash 0.65 0.30 7.2 3.3 10.4 31 Example 4 none 0.2 h, broth 0.56 0.28 6.6 3.3 9.9 33 Example 4 none 4.3 h, broth 0.28 0.09 3.3 1.0 4.4 24 Example 4 none 4.3 h, OA 0.45 0.27 4.0 2.4 6.4 37 Example 4 none 30 h, broth 0.17 0.05 2.0 0.6 2.7 24 Example 4 none 30 h, OA 0.63 0.29 5.7 2.6 8.3 32 Example 4 none 53 h, broth 0.13 0.04 1.5 0.5 2.0 23 Example 4 none 53 h, OA 0.67 0.32 6.0 2.9 8.9 32 Example 4 none 70 h, broth 0.13 0.04 1.5 0.4 1.9 23 Example 4 none 70 h, OA 0.64 0.31 5.8 2.8 8.5 33 Example 5 7.2 ppm liquefied mash 0.11 0.89 1.3 9.9 11.2 89 Example 5 7.2 ppm 0.2 h, broth 0.25 0.83 2.9 9.8 12.8 77 Example 5 7.2 ppm 4.3 h, broth 0.14 0.17 1.6 2.1 3.7 56 Example 5 7.2 ppm 4.3 h, OA 0.02 0.84 0.2 7.9 8.1 97 Example 5 7.2 ppm 30 h, broth 0.08 0.18 1.0 2.1 3.1 68 Example 5 7.2 ppm 30 h, OA 0.04 0.92 0.3 8.6 8.9 96 Example 5 7.2 ppm 53 h, broth 0.07 0.11 0.9 1.3 2.2 61 Example 5 7.2 ppm 53 h, OA 0.08 0.95 0.7 8.9 9.6 93 Example 5 7.2 ppm 70 h, broth 0.08 0.10 0.9 1.2 2.1 55 Example 5 7.2 ppm 70 h, OA 0.05 0.94 0.4 8.8 9.2 95 Example 6 none liquefied mash 0.66 0.34 7.3 3.8 11.1 34 Example 6 none 0.2 h, broth 0.63 0.34 7.6 4.0 11.6 34 Example 6 none 4.3 h, broth 0.33 0.10 3.9 1.2 5.1 23 Example 6 none 4.3 h, OA 0.45 0.27 4.0 2.4 6.4 38 Example 6 none 30 h, broth 0.17 0.06 2.1 0.8 2.8 26 Example 6 none 30 h, OA 0.69 0.33 6.2 3.0 9.1 32 Example 6 none 53 h, broth 0.14 0.05 1.6 0.5 2.2 25 Example 6 none 53 h, OA 0.72 0.35 6.4 3.1 9.5 33 Example 6 none 70 h, broth 0.15 0.05 1.8 0.6 2.4 25 Example 6 none 70 h, OA 0.70 0.34 6.2 3.0 9.2 33

Example 27 Lipase Treatment of Ground Whole Corn Kernels Prior to Liquefaction

Tap water (1377.6 g) was added into each of two jacketed 2-L resin kettles, then 711.9 g wet weight (625.8 g dry weight) of ground whole corn kernels (1.0 mm screen on hammer mill) was added to each kettle with stirring. Each mixture was heated to 55° C. with stirring at 300 rpm, and the pH adjusted to 5.8 with 2 N sulfuric acid. To each mixture was added 21.0 g of an aqueous solution containing 1.008 g of Spezymea FRED L (Genencor®, Palo Alto, Calif.). To one mixture was then added 10.5 mL of aqueous solution of Lipolase® 100L Solution (21 mg total soluble protein, 10 ppm lipase final concentration) and to the second mixture was added 1.05 mL of aqueous solution of Lipolase® 100L Solution (2.1 mg total soluble protein, 1.0 ppm lipase final concentration). Samples were withdrawn from each reaction mixture at 1 h, 2 h, 4 h and 6 h at 55° C., then the temperature of the mixture was increased to 85° C. with stirring at 600 rpm and pH 5.8, and a sample was taken when the mixture first reached 85° C. After 120 minutes at 85° C., a sample was taken and the mixtures were cooled to 50° C. and final samples of the resulting liquefied corn mash were transferred to 50-mL polypropylene centrifuge tubes; all samples were stored frozen at −80° C.

In two separate reactions, a 50 g sample of the 10 ppm lipase-treated liquefied corn mash or a 55 g sample of the 1.0 ppm lipase-treated liquefied corn mash prepared as described above was mixed with oleyl alcohol (OA) (38 g) at 30° C. for 20 h, then the liquefied mash and OA in each reaction mixture were separated by centrifugation and each phase analyzed for wt % lipid (derivatized as fatty acid methyl esters, FAME) and for wt % free fatty acid (FFA, derivatized as fatty acid methyl esters, FAME) according to the method described by Reference 1. The % FFA in the OA phase of the liquefied mash/OA mixture prepared using heat inactivation of 10 ppm lipase during liquefaction was 98% at 20 h, compared to only 62% FFA in the OA phase of the liquefied mash/OA mixture prepared using heat inactivation of 1.0 ppm lipase during liquefaction. Results are shown in Table 11.

TABLE 11 Lipid and free fatty acid content of a mixture of liquefied corn mash and oleyl alcohol, using lipase treatment of ground corn suspension prior to liquefaction (heat inactivation of lipase during liquefaction) reaction lipids FFA lipids FFA lipid + FFA conditions time (h), sample (wt %) (wt %) (mg) (mg) (mg) % FFA 10 ppm lipase 1 h, pre-liquefaction 0.226 0.627 112 311 424 74 at 55° C. prior to 2 h, pre-liquefaction 0.199 0.650 99 323 422 77 liquefaction at 4 h, pre-liquefaction 0.151 0.673 75 334 410 82 85° C., mix with 6 h, pre-liquefaction 0.101 0.700 50 348 398 87 OA for 20 h 0 h, 85° C., liq. mash 0.129 0.764 64 380 444 86 2 h, 85° C., liq. mash 0.129 0.751 64 373 437 85 20 h, 30° C., liq. mash 0.074 0.068 37 34 71 48 20 h, 30° C., OA 0.015 1.035 5.7 394 400 98 1.0 ppm lipase 1 h, pre-liquefaction 0.408 0.480 226 266 492 54 at 55° C. prior to 2 h, pre-liquefaction 0.401 0.424 222 235 457 51 liquefaction at 4 h, pre-liquefaction 0.299 0.433 165 240 405 58 85° C., mix with 6 h, pre-liquefaction 0.346 0.453 192 251 442 57 OA for 20 h 0 h, 85° C., liq. mash 0.421 0.407 233 225 458 49 2 h, 85° C., liq. mash 0.424 0.429 235 237 472 50 20 h, 30° C., liq. mash 0.219 0.054 121 30 151 20 20 h, 30° C., OA 0.344 0.573 140 233 373 62

Example 28 Lipase Screening for Treatment of Ground Whole Corn Kernels Prior to Liquefaction

Seven reaction mixtures containing tap water (67.9 g) and ground whole corn kernels (35.1 g wet wt., ground with 1.0 mm screen using a hammer mill) at pH 5.8 were stirred at 55° C. in stoppered flasks. A 3-mL sample (t=0 h) was removed from each flask and the sample immediately frozen on dry ice, then ca. 0.5 mL of 10 mM sodium phosphate buffer (pH 7.0) containing 1 mg total soluble protein (10 ppm final concentration in reaction mixture) of one of the following lipases (Novozymes) were added to one of each flask: Lipolase® 100 L, Lipex® 100L, Lipoclean® 2000T, Lipozyme® CALB L, Novozyme® CALA L, and Palatase 20000L; no lipase was added to the seventh flask. The resulting mixtures were stirred at 55° C. in stoppered flasks, and 3-mL samples were withdrawn from each reaction mixture at 1 h, 2 h, 4 h and 6 h and immediately frozen in dry ice until analyzed for wt % lipid (derivatized as fatty acid methyl esters, FAME) and for wt % free fatty acid (FFA, derivatized as fatty acid methyl esters, FAME) according to the method described by Reference 1, and the percent free fatty acid content was calculated relative to the total combined concentrations of lipid and free fatty acid was determined for each sample. Results are shown in Table 12.

TABLE 12 Percent free fatty acid content (% FFA) of a mixture of ground whole corn kernels using lipase treatment at 55° C. prior to liquefaction % FFA time 0 h 1 h 2 h 4 h 6 h Lipolase ® 100L 33 56 74 76 79 Lipex ® 100L 34 66 81 83 83 Lipoclean ® 2000T 38 55 73 69 65 Lipozyme ® CALB L 39 38 37 43 41 Novozyme ® CALA L 37 40 44 44 45 Palatase ® 20000L 37 49 59 62 66 no enzyme 38 33 37 41 42

Example 29 Lipase Treatment of Ground Whole Corn Kernels Prior to Simultaneous Saccharification and Fermentation with In-Situ Product Removal Using Oleyl Alcohol

Three fermentations were run as described above in Examples 7, 8, and 10. For fermentations run as described in Examples 7 and 10, lipase (10 ppm of Lipolase® total soluble protein) was added to the suspension of ground corn and heated at 55° C. for 6 h prior to Liquefaction to produce a liquefied corn mash containing heat-inactivated lipase. No lipase was added to the suspension of ground corn used to prepare liquefied corn mash for the fermentation described in Example 8, but the suspension was subjected to the same heating step at 55° C. prior to liquefaction. The % FFA in lipase-treated liquefied corn mash prepared for fermentations run as described in Examples 7 and 10 was 83% and 86%, respectively, compare to 41% without lipase treatment (Example 8). Over the course of the fermentations, the concentration of FFA did not decrease in any of the fermentations, including that containing heat-inactivated lipase. The % FFA in the OA phase of the fermentation run according to Examples 7 and 10 (with heat inactivation of lipase prior to fermentation) were each 97% at 70 h (end of run (EOR)), compared to only 49% FFA for the fermentation run according to Example 8 where ground whole corn kernels had not been treated with lipase prior to liquefaction. Results are shown in Table 13.

TABLE 13 Lipid and free fatty acid content of fermentations containing oleyl alcohol as ISPR extractant and heat-inactivated lipase (lipase treatment of ground corn suspension prior to liquefaction) lipids FFA lipids FFA lipid + fermentation lipase time (h), sample (wt %) (wt %) (g) (g) FFA (g) % FFA Example 7 10 ppm pre-lipase/pre-liq. 0.65 0.22 7.1 2.4 9.4 25 Example 7 10 ppm post-lipase/pre-liq. 0.22 0.65 2.4 7.0 9.5 74 Example 7 10 ppm liquefied mash 0.17 0.79 1.8 8.5 10.3 83 Example 7 10 ppm 0.3 h, broth 0.16 0.79 1.8 8.9 10.7 83 Example 7 10 ppm 4.8 h, broth 0.14 0.31 1.6 3.5 5.1 69 Example 7 10 ppm 4.8 h, OA 0.04 0.68 0.3 5.4 5.6 95 Example 7 10 ppm 29 h, broth 0.10 0.12 1.2 1.3 2.5 53 Example 7 10 ppm 29 h, OA 0.03 1.05 0.2 8.2 8.4 98 Example 7 10 ppm 53 h, broth Example 7 10 ppm 53 h, OA 0.07 1.14 0.5 9.0 9.5 95 Example 7 10 ppm 70 h, broth 0.11 0.07 1.2 0.8 2.0 39 Example 7 10 ppm 70 h, OA 0.03 1.10 0.2 8.7 8.9 97 Example 8 none pre-lipase/pre-liq. 0.62 0.23 6.7 2.5 9.2 27 Example 8 none post-lipase/pre-liq. 0.57 0.26 6.2 2.8 9.0 31 Example 8 none liquefied mash 0.52 0.36 5.6 4.0 9.6 41 Example 8 none 0.3 h, broth 0.50 0.33 5.7 3.8 9.4 40 Example 8 none 4.8 h, broth 0.47 0.14 5.3 1.6 6.9 24 Example 8 none 4.8 h, OA 0.12 0.32 1.0 2.9 3.9 73 Example 8 none 29 h, broth 0.30 0.05 3.4 0.6 4.0 16 Example 8 none 29 h, OA 0.31 0.46 2.7 4.1 6.9 60 Example 8 none 53 h, broth Example 8 none 53 h, OA 0.47 0.50 4.2 4.4 8.6 51 Example 8 none 70 h, broth 0.22 0.04 2.5 0.5 3.0 17 Example 8 none 70 h, OA 0.40 0.39 3.6 3.5 7.0 49 Example 10 10 ppm pre-lipase/pre-liq. 0.67 0.23 7.4 2.5 9.9 25 Example 10 10 ppm post-lipase/pre-liq. 0.19 0.69 2.1 7.6 9.7 78 Example 10 10 ppm liquefied mash 0.14 0.85 1.6 9.4 11.0 86 Example 10 10 ppm 0.3 h, broth 0.13 0.82 1.5 9.4 10.9 86 Example 10 10 ppm 4.8 h, broth 0.11 0.29 1.3 3.3 4.6 72 Example 10 10 ppm 4.8 h, OA 0.04 0.60 0.3 5.2 5.6 94 Example 10 10 ppm 29 h, broth 0.09 0.14 1.0 1.6 2.6 61 Example 10 10 ppm 29 h, OA 0.01 0.96 0.1 8.4 8.5 99 Example 10 10 ppm 53 h, broth Example 10 10 ppm 53 h, OA 0.02 0.95 0.2 8.3 8.4 98 Example 10 10 ppm 70 h, broth 0.09 0.08 1.1 0.9 1.9 45 Example 10 10 ppm 70 h, OA 0.03 0.99 0.3 8.7 9.0 97

Example 30 Lipase Treatment of Ground Whole Corn Kernels or Liquefied Corn Mash for Simultaneous Saccharification and Fermentation with In-Situ Product Removal Using Corn Oil Fatty Acids (COFA)

Five fermentations were run as described above in Examples 9, 11, 12, 13, and 14. For the fermentations run as described in Examples 9, 13, and 14, lipase (10 ppm of Lipolase® total soluble protein) was added after Liquefaction and there was no heat-inactivation of lipase. Fermentations run as described in Examples 9 and 14 had 5 g/L of ethanol added prior to inoculation, whereas the fermentation run as described in Example 13 had no added ethanol. The fermentations run as described in Examples 11 and 12 employed the addition of 10 ppm Lipolase® total soluble protein to the suspension of ground corn prior to liquefaction, resulting in heat inactivation of lipase during liquefaction. The fermentation run as described in Example 11 had 5 g/L of ethanol added prior to inoculation, whereas the fermentation run as described in Example 12 had no added ethanol. The final total grams of isobutanol (i-BuOH) present in the COFA phase of the fermentations containing active lipase was significantly greater than the final total grams of i-BuOH (including i-BuOH present as FABE) present in the COFA phase of the fermentations containing inactive lipase. The final total grams of isobutanol (i-BuOH) present in the fermentation broths (aqueous phase) containing active lipase were only slightly less than the final total grams of i-BuOH present in the fermentation broths containing inactive lipase, such that the overall production of i-BuOH (as a combination of free i-BuOH and isobutyl esters of COFA (FABE)) was significantly greater in the presence of active lipase when compared to that obtained in the presence of heat-inactivated lipase. Results are shown in Tables 14 and 15.

TABLE 14 Dependence of the production of free isobutanol (i-BuOH) and isobutyl esters of COFA (FABE) in fermentations containing corn oil fatty acids (COFA) as ISPR extractant in presence (Examples 9, 13, and 14) or absence (Examples 11 and 12) of active lipase (COFA phase analysis) g i-BuOH fermenta- from total g fermenta- tion g i-BuOH/ g FABE/ FABE/ i-BuOH/ tion time (h) kg COFA kg COFA kg COFA kg COFA Example 9 4.5 2.4 0.0 0 2.4 Example 9 28.8 5.4 70.9 16.5 22.0 Example 9 52.4 8.9 199.0 46.4 55.3 Example 9 69.3 4.9 230.9 53.9 69.3 Example 11 6.6 2.3 0.0 0.0 2.3 Example 11 53.5 25.1 2.9 0.6 25.7 Example 11 71.1 24.4 6.3 1.4 25.8 Example 12 6.6 2.3 0.0 0.0 2.3 Example 12 53.5 12.8 1.6 0.4 13.2 Example 12 71.1 12.8 3.0 0.7 13.5 Example 13 6.6 2.3 0.0 0.0 2.3 Example 13 53.5 4.9 72.1 16.0 20.9 Example 13 71.1 4.6 91.4 20.3 24.9 Example 14 6.6 2.1 0.0 0.0 2.1 Example 14 53.5 9.8 197.2 43.8 53.6 Example 14 71.1 4.9 244.5 54.3 59.2

TABLE 15 Dependence of the production of free isobutanol (i-BuOH) and isobutyl esters of COFA (FABE) in fermentations containing corn oil fatty acids (COFA) as ISPR extractant on presence (Examples 9, 13 and 14) or absence (Examples 11 and 12) of active lipase (fermentation broth analysis) g i-BuOH fermenta- from total g tion g i-BuOH/ g FABE/ FABE/ i-BuOH/ sample time (h) kg broth kg broth kg broth kg broth Example 9 4.5 0.0 0.0 0 0 Example 9 28.8 0.0 12.6 2.9 2.9 Example 9 52.4 0.0 30.3 7.1 7.1 Example 9 69.3 0.0 24.7 5.8 5.8 Example 11 6.6 0.0 0.0 0 0.0 Example 11 53.5 9.8 0.0 0 9.8 Example 11 71.1 9.5 0.0 0 9.5 Example 12 6.6 0.0 0.0 0 0 Example 12 53.5 3.8 0.0 0.0 3.8 Example 12 71.1 5.1 0.0 0.0 5.1 Example 13 6.6 0.0 0.0 0 0 Example 13 53.5 2.1 3.0 0.7 2.8 Example 13 71.1 2.1 7.4 1.6 3.7 Example 14 6.6 0.0 0.0 0 0.0 Example 14 53.5 2.9 22.4 5.0 7.9 Example 14 71.1 3.3 19.3 4.3 7.6

Example 31 Production of Iso-Butyl COFA Esters by Phospholipase-Catalyzed Reaction of Iso-Butanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.3), isobutanol (2-methyl-1-propanol), phospholipase (Phospholipase A; SigmaAldrich, L3295-250) and corn oil fatty acids prepared from corn oil were stirred at 30° C. (Table 16), and samples were withdrawn from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for isobutanol (i-BuOH) and isobutyl esters of corn oil fatty acids (i-BuO-COFA) (Table 17).

TABLE 16 Reaction conditions for conversion of isobutanol (i-BuOH) to isobutyl esters of corn oil fatty acids (i-BuO-COFA) MES buffer i-BuOH COFA lipase reaction (0.2M) (g) (g) (g) (ppm) 1 46.1 3.6 14.7 10 2 46.1 3.6 14.7 3 3 46.1 3.6 14.7 0

TABLE 17 Weights of isobutanol (i-BuOH) and isobutyl esters of corn oil fatty acids (i-BuO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 16. i-BuOH i-BuO- total i- total i- free i- from i- COFA reac- time BuOH BuOH (g) BuOH (g) BuO-COFA (g) tion (h) (g) (AQ) (ORG) (ORG) (g) (ORG) (ORG) 1 0.1 1.29 2.39 2.39 0.00 0.00 1 2 1.24 2.44 2.38 0.06 0.26 1 20 1.25 2.43 2.22 0.21 0.96 1 24 1.26 2.42 2.19 0.23 1.03 1 44 1.27 2.41 2.13 0.28 1.28 1 48 1.22 2.46 2.15 0.31 1.41 2 0.1 1.27 2.34 2.34 0.00 0.00 2 2 1.25 2.35 2.33 0.02 0.08 2 20 1.24 2.37 2.30 0.07 0.30 2 24 1.22 2.38 2.31 0.07 0.32 2 44 1.33 2.28 2.18 0.10 0.44 2 48 1.23 2.38 2.27 0.11 0.48 3 0.1 1.27 2.33 2.33 0.00 0.00 3 2 1.26 2.34 2.34 0.00 0.00 3 20 1.22 2.38 2.37 0.01 0.07 3 24 1.25 2.35 2.33 0.02 0.08 3 44 1.24 2.36 2.32 0.04 0.18 3 48 1.24 2.36 2.32 0.04 0.18

Example 32 Dependence of Isobutyl-COFA Ester Concentration on Aqueous/COFA Ratio in Lipase-Catalyzed Reactions

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.2), isobutanol (2-methyl-1-propanol), lipase (Lipolase® 100 L; Novozymes) and corn oil fatty acids prepared from corn oil (Table 18) were stirred at 30° C., and samples were withdrawn from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for isobutanol (i-BuOH) and isobutyl esters of corn oil fatty acids (i-BuO-COFA) (Table 19).

TABLE 18 Reaction conditions for conversion of isobutanol (i-BuOH) to isobutyl esters of corn oil fatty acids (i-BuO-COFA) reaction MES buffer i-BuOH COFA lipase # (0.2M) (g) (g) (g) (ppm) 1 45.96 3.6 43.4 10 2 45.96 3.6 21.7 10 3 45.96 3.6 10.85 10 4 45.96 3.6 43.4 4 5 45.96 3.6 43.4 0

TABLE 19 Weights of isobutanol (i-BuOH) and isobutyl esters of corn oil fatty acids (i-BuO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 18 i-BuOH i-BuO- total i- total i- free i- from i- COFA reac- time BuOH BuOH (g) BuOH (g) BuO-COFA (g) tion (h) (g) (AQ) (ORG) (ORG) (g) (ORG) (ORG) 1 0.1 0.77 2.83 2.77 0.05 0.24 1 1 0.76 2.84 2.58 0.25 1.13 1 2 0.74 2.86 2.41 0.44 2.00 1 4 0.66 2.94 2.05 0.89 4.03 1 6 0.63 2.97 1.43 1.54 6.93 1 21.5 0.28 3.32 0.34 2.98 13.4 1 25.5 0.23 3.37 0.29 3.08 13.8 2 0.1 1.17 2.43 2.36 0.07 0.30 2 1 1.09 2.51 2.26 0.24 1.10 2 2 1.07 2.53 2.19 0.34 1.52 2 4 1.03 2.57 1.99 0.59 2.64 2 6 1.00 2.60 1.70 0.90 4.04 2 21.5 0.75 2.85 0.58 2.27 10.2 2 25.5 0.59 3.01 0.49 2.52 11.4 3 0.1 1.56 2.04 1.98 0.06 0.27 3 1 1.55 2.05 1.77 0.28 1.24 3 2 1.49 2.11 1.65 0.46 2.08 3 4 1.45 2.15 1.28 0.87 3.92 3 6 1.33 2.27 0.96 1.31 5.92 3 21.5 1.12 2.48 0.26 2.22 10.0 3 25.5 0.88 2.72 0.26 2.46 11.1 4 0.1 0.84 2.76 2.75 0.02 0.07 4 1 0.78 2.82 2.73 0.09 0.40 4 2 0.83 2.77 2.59 0.17 0.79 4 4 0.78 2.82 2.44 0.38 1.71 4 6 0.78 2.82 2.10 0.72 3.25 4 21.5 0.58 3.02 1.12 1.90 8.57 4 25.5 0.51 3.09 0.97 2.11 9.51 5 0.1 0.90 2.70 2.70 0.00 0.00 5 1 0.90 2.70 2.70 0.00 0.00 5 2 0.92 2.68 2.68 0.00 0.00 5 4 0.89 2.71 2.70 0.00 0.02 5 6 0.92 2.68 2.62 0.06 0.29 5 21.5 0.90 2.70 2.62 0.08 0.37 5 25.5 0.89 2.71 2.62 0.09 0.41

Example 33 Dependence of Butyl-COFA Ester Concentration on Esterification Alcohol in Lipase-Catalyzed Reactions

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.2), isobutanol (2-methyl-1-propanol) or n-butanol, lipase (Lipolase® 100 L; Novozymes) and corn oil fatty acids prepared from corn oil (Table 20) were stirred at 30° C., and samples were withdrawn from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for isobutanol (i-BuOH) or n-butanol (n-BuOH) and isobutyl- or butyl esters of corn oil fatty acids (BuO-COFA) (Table 21).

TABLE 20 Reaction conditions for conversion of isobutanol (i-BuOH) or n-butanol (n-BuOH) to butyl esters of corn oil fatty acids (BuO-COFA) MES buffer butanol COFA lipase Reaction butanol (0.2M) (g) (g) (g) (ppm) 6 iso-butanol 45.96 3.6 13.5 10 7 n-butanol 45.96 3.6 13.5 10 8 iso-butanol 45.96 3.6 13.5 0 9 isobutanol 45.96 3.6 13.5 4

TABLE 21 Weights of isobutanol (i-BuOH) or n-butanol (n-BuOH) and butyl esters of corn oil fatty acids (BuO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 20 reac- time tion (h) i-BuOH i-BuO- total i- total i- i-BuOH from i- COFA BuOH BuOH (g) BuO-COFA (g) (g) (AQ) (g) (ORG) (ORG) (g) (ORG) (ORG) 6 0.1 1.46 2.14 2.11 0.04 0.16 6 2 1.41 2.19 1.63 0.56 2.51 6 4 1.27 2.33 1.31 1.02 4.58 6 21 0.66 2.94 0.29 2.65 12.0 6 25 0.60 3.00 0.26 2.73 12.3 6 46 0.54 3.06 0.22 2.83 12.8 n-BuOH n-BuO- total n- total n- n-BuOH from n- COFA BuOH BuOH (g) BuO-COFA (g) (g) (AQ) (g) (ORG) (ORG) (g) (ORG) (ORG) 7 0.1 1.31 2.29 2.26 0.03 0.11 7 2 1.26 2.34 1.89 0.45 2.03 7 4 1.20 2.40 1.66 0.74 3.35 7 21 0.81 2.79 0.50 2.29 10.3 7 25 0.77 2.83 0.40 2.43 11.0 7 46 0.50 3.10 0.23 2.87 12.9 i-BuOH i-BuO- total i- total i- i-BuOH from i- COFA BuOH BuOH (g) BuO-COFA (g) (g) (AQ) (g) (ORG) (ORG) (g) (ORG) (ORG) 8 0.1 1.62 1.98 1.98 0.00 0.01 8 2 1.56 2.04 2.04 0.00 0.00 8 4 1.59 2.01 2.01 0.00 0.00 8 21 1.59 2.01 2.00 0.01 0.04 8 25 1.55 2.05 2.04 0.01 0.04 8 46 1.45 2.15 2.12 0.02 0.11 i-BuOH i-BuO- total i- total i- i-BuOH from i- COFA BuOH BuOH (g) BuO-COFA (g) (g) (AQ) (g) (ORG) (ORG) (g) (ORG) (ORG) 9 0.1 1.57 2.03 2.02 0.01 0.04 9 2 1.54 2.06 1.86 0.19 0.86 9 4 1.44 2.16 1.79 0.36 1.64 9 21 1.14 2.46 0.95 1.51 6.82 9 25 1.10 2.50 0.83 1.67 7.50 9 46 0.78 2.82 0.44 2.37 10.7

Example 34 Production of Iso-Butyl Oleate by Lipase-Catalyzed Reaction of Isobutanol and Oleic Acid

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.2), isobutanol (2-methyl-1-propanol), lipase (0 ppm or 10 ppm Lipolase® 100 L; Novozymes) and oleic acid (Alfa Aesar) (Table 22) were stirred at 30° C., and samples were withdrawn from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for isobutanol (i-BuOH) and iso-butyl oleate (i-BuO-oleate) (Table 23).

TABLE 22 Reaction conditions for conversion of isobutanol (i-BuOH) to iso-butyl oleate (i-BuO-oleate) reaction MES buffer i-BuOH oleic acid lipase # (0.2M) (g) (g) (g) (ppm) 10 46.11 3.64 14.62 10 11 46.10 3.59 14.40 0

TABLE 23 Weights of isobutanol (i-BuOH) and iso-butyl oleate (i- BuO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 22 i-BuOH i-BuO- total i- total i- i-BuOH from i- oleate reac- time BuOH BuOH (g) (g) BuO-oleate (g) tion (h) (g) (AQ) (ORG) (ORG) (g) (ORG) (ORG) 10 0.1 1.37 2.28 2.24 0.04 0.18 10 2 1.30 2.34 1.95 0.40 1.81 10 4 1.28 2.37 1.82 0.55 2.53 10 6 1.22 2.42 1.71 0.72 3.27 10 23 0.92 2.72 0.71 2.01 9.20 10 27 0.89 2.75 0.65 2.11 9.62 10 47 0.81 2.84 0.55 2.29 10.5 10 51 0.82 2.83 0.54 2.29 10.5 11 0.1 1.44 2.16 2.16 0.00 0.00 11 2 1.45 2.15 2.15 0.00 0.00 11 4 1.44 2.16 2.16 0.00 0.00 11 6 1.43 2.16 2.16 0.00 0.00 11 23 1.49 2.10 2.10 0.01 0.02 11 27 1.46 2.14 2.13 0.01 0.04 11 47 1.48 2.12 2.09 0.02 0.10 11 51 1.52 2.07 2.05 0.02 0.11

Example 35 Comparison of Production of Iso-Butyl Oleate by Lipase-Catalyzed Reactions of Isobutanol and Oleic Acid

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (MES, 0.20 M, pH 5.2), isobutanol (2-methyl-1-propanol), oleic acid (Alfa Aesar), and lipase (10 ppm) from Lipolase® 100L, Lipex® 100L, Lipozyme® CALB L, Novozyme® CALA L, Palatase® from Novozymes, or lipase (10 ppm) from Pseudomonas fluorescens, Pseudomonas cepacia, Mucor miehei, hog pancreas, Candida cylindracea, Rhizopus niveus, Candida antarctica, Rhizopus arrhizus or Aspergillus from SigmaAldrich (Table 24), were stirred at 30° C., and samples were withdrawn from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for isobutanol (i-BuOH) and iso-butyl oleate (i-BuO-oleate) (Table 25).

TABLE 24 Reaction conditions for conversion of isobutanol (i-BuOH) to iso-butyl oleate (i-BuO-oleate) MES buffer i-BuOH oleic acid lipase (0.2M) (g) (g) (g) (ppm) 46.105 3.601 13.72 10

TABLE 25 Weights of isobutanol (i-BuOH) and iso-butyl oleate (i-BuO-oleate) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 24 total i- total i- i-BuOH from i-BuO- BuOH BuOH i-BuOH i-BuO-oleate oleate lipase time (h) (g) (AQ) (g) (ORG) (g) (ORG) (g) (ORG) (g) (ORG) Lipolase ® 100L 23 0.92 2.72 0.71 2.01 9.20 Lipex ® 100L 23 0.65 2.95 0.30 2.65 12.09 Lipozyme ® CALB L 23 1.01 2.59 0.82 1.77 8.08 Novozyme ® CALA L 23 1.39 2.22 2.16 0.06 0.27 Palatase ® 23 1.27 2.33 1.43 0.91 4.14 Pseudomonas fluorescens 23 1.38 2.22 1.97 0.25 1.14 Pseudomonas cepacia 23 1.39 2.21 1.95 0.26 1.20 Mucor miehei 23 1.29 2.31 1.57 0.75 3.42 hog pancreas 23 1.40 2.20 2.19 0.01 0.04 Candida cylindracea 23 1.15 2.45 1.08 1.37 6.25 Rhizopus niveus 23 1.39 2.21 2.19 0.02 0.11 Candida antarctica 23 1.37 2.24 2.08 0.15 0.69 Rhizopus arrhizus 23 1.01 2.59 0.81 1.78 8.12 Aspergillus 23 1.36 2.24 2.06 0.18 0.82 no lipase 23 1.49 2.10 2.10 0.01 0.02

Example 36 Production of Ethyl-COFA Ester by Lipase-Catalyzed Reaction of Ethanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.5), ethanol, lipase (Lipolase® 100 L or Lipozyme® CALB L; Novozymes) and corn oil fatty acids prepared from corn oil (Table 26) were stirred at 30° C., and samples were withdrawn while stirring from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for ethanol and ethyl esters of corn oil fatty acids (EtO-COFA) (Table 27).

TABLE 26 Reaction conditions for conversion of ethanol (EtOH) to ethyl esters of corn oil fatty acids (EtO-COFA) MES buffer ethanol COFA lipase Reaction (0.2M) (g) (g) (g) lipase (ppm) 12 46.11 3.60 14.48 Lipolase ® 10 100L 13 46.10 3.60 14.47 Lipozyme ® 10 CALB L 14 46.11 3.61 14.47 no lipase 0

TABLE 27 Weights of ethanol (EtOH) and ethyl esters of corn oil fatty acids (EtO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 26 EtOH total total from EtO- ETO- reac- time EtOH EtOH EtOH COFA COFA tion (h) (g) (AQ) (g) (ORG) (g) (ORG) (g) (ORG) (g) (ORG) 12 0 2.94 0.655 0.634 0.021 0.01 12 2 3.09 0.504 0.105 0.398 0.81 12 20 2.74 0.854 0.030 0.824 4.46 12 24 2.43 1.167 0.032 1.135 5.25 12 44 2.37 1.230 0.022 1.208 7.28 12 48 2.24 1.360 0.022 1.338 7.63 13 0 2.94 0.659 0.635 0.024 0.01 13 2 2.83 0.773 0.074 0.699 1.88 13 20 2.10 1.501 0.000 1.501 9.72 13 24 2.07 1.532 0.000 1.532 10.14 13 44 1.94 1.673 0.014 1.659 10.93 13 48 1.72 1.882 0.016 1.865 11.05 14 0 2.96 0.646 0.624 0.023 0.01 14 2 2.93 0.679 0.661 0.018 0.01 14 20 2.75 0.857 0.779 0.079 0.02 14 24 2.87 0.738 0.662 0.075 0.03 14 44 2.79 0.813 0.688 0.126 0.04 14 48 2.82 0.785 0.671 0.114 0.05

Example 37 Production of Ethyl-COFA Ester by Lipase-Catalyzed Reaction of Ethanol and Corn Oil Fatty Acids (COFA) During Fermentation of Yeast

The wild-type yeast strain CEN.PK113-7D was propagated overnight in medium containing yeast nitrogen base without amino acids (6.7 g/L), dextrose (25 g/L), and MES buffer (0.1 M at pH 5.5). The overnight culture was diluted into fresh medium such that the resulting optical density at 600 nm was 0.1. The diluted culture was aliquoted, 25 mL per flask, into six 250 mL sealed-cap shake flasks. Four of the cultures were supplemented with either of two lipase enzyme stock solutions (2 mg protein/mL 10 mM phosphate buffer (pH 7.0) of Lipozyme® CALB L or Lipolase® 100L) to a final lipase concentration of 10 ppm in the media. Corn oil fatty acids (COFA) were added at a 1:1 volume ratio to the aqueous culture in three of the flasks (no enzyme, CALB L, or Lipolase® 100L). One flask had no supplements. The cultures were grown in a temperature-controlled shaking incubator at 30° C. and a shaking speed of 250 rpm for 23 hours. Samples for cell mass determination were allowed to phase separate in 15 mL conical bottom tubes. The sample's optical density at 600 nm was measured at a 20-fold dilution in saline. Samples (5 mL aqueous or 10 mL culture/COFA emulsion) for chromatographic analysis were immediately centrifuged for 5 minutes at 4000 rpm in a TX-400 swinging bucket rotor in 15 mL conical bottom tubes. For aqueous samples, a 0.22 m spin filter was used prior to analysis. Aqueous samples were analyzed on a Shodex SH1011 column with a SH-G guard column using 0.01 M sulfuric acid mobile phase at 50° C. and a flow rate of 0.5 mL per minute. Detection of sugars and alcohols was by Refractive Index and 210 nm absorption, and quantitation was performed using standard curves. Samples were taken of the aqueous culture (no added COFA) or culture/COFA emulsion, and analyzed as described in previous Examples for ethyl esters of COFA. Results are shown in Tables 28 and 29.

TABLE 28 Weights of ethanol (EtOH), glucose and fermentation byproducts present in the aqueous media (AQ) from 23 h fermentations glucose glycerol acetate acetoin EtOH (g/L) (g/L) (g/L) (g/L) (g/L) Media 0 0.62 1.01 0.08 9.98 media + CALB L 0 0.72 0.94 0.06 9.94 media + Lipolase ® 100L 0 0.61 0.99 0.05 9.87 media + COFA 0 0.68 0.32 0.15 7.73 media + COFA + CALB L 0 0.74 0.09 0.11 3.92 media + COFA + 0 0.63 0.23 0.18 7.19 Lipolase ® 100L

TABLE 29 Weights of ethanol (EtOH) and ethyl esters of corn oil fatty acids (EtO-COFA) present in the aqueous fraction (AQ) and the organic fraction (ORG) for 23 h fermentations EtOH from EtOH EtOH EtO-COFA ETO-COFA (g/L) (g/L) (g/L) (g/L) Reaction (AQ) (ORG) (ORG) (ORG) media + COFA 6.7 0 0.18 1.2 media + COFA + CALB L 3.4 0 4.52 30.0 media + COFA + 6.1 0 0.72 4.8 Lipolase ® 100L

Example 38 Production of Methyl-COFA Ester by Lipase-Catalyzed Reaction of Methanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.5), methanol, lipase (Lipolase® 100 L (Novozymes), Lipozyme® CALB L (Novozymes), Rhizopus arrhizus lipase (SigmaAldrich), and Candida cylindracea lipase (SigmaAldrich) and corn oil fatty acids prepared from corn oil (Table 30) were stirred at 30° C., and samples were withdrawn while stirring from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for ethanol and ethyl esters of corn oil fatty acids (EtO-COFA) (Table 31).

TABLE 30 Reaction conditions for conversion of methanol (MeOH) to methyl esters of corn oil fatty acids (MeO-COFA) MES buffer methanol COFA lipase Reaction (0.2M) (g) (g) (g) lipase (ppm) 15 46.11 3.60 14.51 Lipolase ® 10 100L 16 46.10 3.59 14.49 Lipozyme ® 10 CALB L 17 46.11 3.60 14.49 R. arrhizus 10 18 46.10 3.60 14.48 C. cylindracea 10 19 46.10 3.60 14.51 no lipase 10

TABLE 31 Weights of methanol (MeOH) and methyl esters of corn oil fatty acids (MeO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 30 MeOH MeO- total total MeOH from MeO- COFA reac- time MeOH MeOH (g) COFA (g) tion (h) (g) (AQ) (g) (ORG) (ORG) (g) (ORG) (ORG) 15 0 3.33 0.26 0.05 0.01 0.02 15 2 3.09 0.50 0.05 0.13 0.16 15 4 3.09 0.51 0.04 0.33 0.73 15 20 2.81 0.79 0.04 0.70 3.03 15 24 2.72 0.87 0.04 0.79 3.47 15 44 2.53 1.06 0.03 1.00 4.97 15 48 2.48 1.12 0.03 1.05 5.18 16 0 3.07 0.53 0.04 0.02 0.02 16 2 3.01 0.59 0.04 0.20 0.22 16 4 2.92 0.67 0.03 0.56 1.32 16 20 2.54 1.06 0.03 0.99 5.25 16 24 2.43 1.16 0.03 1.09 5.90 16 44 2.28 1.32 0.02 1.27 7.63 16 48 2.22 1.37 0.03 1.32 7.89 17 0 3.09 0.52 0.04 0.02 0.02 17 2 3.05 0.56 0.06 0.05 0.06 17 4 2.98 0.63 0.04 0.25 0.24 17 20 3.03 0.57 0.04 0.32 0.49 17 24 2.98 0.63 0.04 0.35 0.52 17 44 2.99 0.62 0.04 0.38 0.62 17 48 2.94 0.67 0.04 0.40 0.61 18 0 3.17 0.43 0.05 0.02 0.02 18 2 3.12 0.49 0.04 0.02 0.02 18 4 2.96 0.64 0.00 0.64 1.24 18 20 2.64 0.96 0.03 0.89 3.97 18 24 2.58 1.03 0.03 0.95 4.49 18 44 2.37 1.23 0.03 1.18 6.40 18 48 2.30 1.30 0.03 1.25 6.71 19 0 3.08 0.52 0.04 0.03 0.02 19 2 3.08 0.52 0.04 0.02 0.02 19 4 3.04 0.56 0.04 0.03 0.02 19 20 3.08 0.53 0.04 0.03 0.03 19 24 3.04 0.56 0.05 0.03 0.04 19 44 3.01 0.59 0.04 0.06 0.04 19 48 2.95 0.65 0.05 0.06 0.04

Example 39 Production of 1-Propyl-COFA Ester by Lipase-Catalyzed Reaction of 1-Propanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.5), 1-propanol, lipase (Lipolase® 100 L (Novozymes), Lipozyme® CALB L (Novozymes), Rhizopus arrhizus lipase (SigmaAldrich), and Candida cylindracea lipase (SigmaAldrich) and corn oil fatty acids prepared from corn oil (Table 32) were stirred at 30° C., and samples were withdrawn while stirring from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for 1-propanol and 1-propyl esters of corn oil fatty acids (PrO-COFA) (Table 33).

TABLE 32 Reaction conditions for conversion of 1-propanol (PrOH) to 1-propyl esters of corn oil fatty acids (PrO-COFA) MES buffer 1-propanol COFA lipase Reaction (0.2M) (g) (g) (g) lipase (ppm) 20 46.11 3.60 14.47 Lipolase ® 10 100L 21 46.12 3.60 14.48 Lipozyme ® 10 CALB L 22 46.10 3.60 14.48 R. arrhizus 10 23 46.13 3.62 14.49 C. cylindracea 10 24 46.13 3.60 14.48 no lipase 0

TABLE 33 Weights of 1-propanol (PrOH) and 1-propyl esters of corn oil fatty acids (PrO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 32 PrOH total total from PrO- PrO- reac- time PrOH PrOH PrOH COFA (g) COFA (g) tion (h) (g) (AQ) (g) (ORG) (g) (ORG) (ORG) (ORG) 20 0 2.54 1.05 0.80 0.00 0.02 20 2 2.39 1.20 0.70 0.11 0.44 20 4 2.00 1.60 0.61 0.55 1.88 20 20 1.65 1.95 0.31 1.50 6.96 20 24 1.51 2.08 0.28 1.69 7.97 20 44 1.13 2.46 0.16 2.23 11.09 20 48 1.09 2.51 0.15 2.29 11.27 21 0 2.44 1.16 0.79 0.00 0.02 21 2 2.38 1.22 0.65 0.13 0.49 21 4 2.07 1.53 0.52 0.73 2.94 21 20 1.16 2.43 0.17 2.18 10.80 21 24 1.08 2.51 0.16 2.28 11.26 21 44 1.00 2.60 0.13 2.40 11.86 21 48 0.98 2.62 0.13 2.42 11.91 22 0 2.49 1.11 0.80 0.00 0.02 22 2 2.42 1.18 0.76 0.10 0.38 22 4 2.23 1.37 0.71 0.29 1.08 22 20 2.09 1.51 0.56 0.71 2.96 22 24 2.06 1.54 0.54 0.77 3.17 22 44 1.87 1.73 0.47 0.58 1.75 22 48 1.88 1.73 0.46 0.60 1.82 23 0 2.49 1.13 0.80 0.00 0.02 23 2 2.45 1.17 0.77 0.07 0.29 23 4 2.35 1.27 0.71 0.21 0.82 23 20 2.00 1.61 0.50 0.89 3.74 23 24 1.93 1.68 0.49 0.99 4.23 23 44 1.57 2.04 0.33 1.56 6.83 23 48 1.49 2.13 0.31 1.67 7.33 24 0 2.49 1.11 0.81 0.00 0.02 24 2 2.47 1.13 0.81 0.00 0.02 24 4 2.38 1.21 0.78 0.01 0.03 24 20 2.46 1.14 0.79 0.01 0.05 24 24 2.42 1.17 0.79 0.01 0.05 24 44 2.41 1.19 0.76 0.02 0.09 24 48 2.32 1.28 0.77 0.03 0.10

Example 40 Production of 1-Pentyl-COFA Ester by Lipase-Catalyzed Reaction of 1-Pentanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.5), 1-pentanol, lipase (Lipolase® 100 L (Novozymes), Lipozyme® CALB L (Novozymes), Rhizopus arrhizus lipase (SigmaAldrich), and Candida cylindracea lipase (SigmaAldrich) and corn oil fatty acids prepared from corn oil (Table 34) were stirred at 30° C., and samples were withdrawn while stirring from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for 1-pentanol and 1-pentyl esters of corn oil fatty acids (PenO-COFA) (Table 35).

TABLE 34 Reaction conditions for conversion of 1-pentanol (PenOH) to 1-pentyl esters of corn oil fatty acids (PenO-COFA) MES buffer 1-pentanol COFA lipase Reaction (0.2M) (g) (g) (g) lipase (ppm) 25 46.11 3.60 14.47 Lipolase ® 10 100L 26 46.12 3.60 14.48 Lipozyme ® 10 CALB L 27 46.10 3.60 14.48 R. arrhizus 10 28 46.13 3.62 14.49 C. cylindracea 10 29 46.13 3.60 14.48 no lipase 0

TABLE 35 Weights of 1-pentanol (PenOH) and 1-pentyl esters of corn oil fatty acids (PenO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 34 PenOH PenO- total total from PenO- COFA reac- time PenOH PenOH PenOH COFA (g) (g) tion (h) (g) (AQ) (g) (ORG) (g) (ORG) (ORG) (ORG) 25 0 0.364 3.238 3.091 0.002 0.006 25 2 0.339 3.264 2.745 0.446 1.760 25 4 0.373 3.229 2.761 0.557 2.196 25 20 0.336 3.266 1.833 1.002 3.953 25 24 0.325 3.277 1.575 1.257 4.960 25 44 0.226 3.377 0.921 2.383 9.400 25 48 0.206 3.396 0.723 2.524 9.957 26 0 0.364 3.243 3.105 0.002 0.006 26 2 0.317 3.290 2.462 0.512 2.019 26 4 0.320 3.287 2.287 0.652 2.574 26 20 0.130 3.477 0.387 3.007 11.860 26 24 0.094 3.513 0.215 3.251 12.823 26 44 0.075 3.532 0.165 3.312 13.067 26 48 0.081 3.526 0.165 3.326 13.120 27 0 0.384 3.216 3.102 0.002 0.006 27 2 0.356 3.244 2.957 0.437 1.725 27 4 0.333 3.267 2.912 0.388 1.532 27 20 0.363 3.237 2.664 0.433 1.707 27 24 0.367 3.233 2.597 0.665 2.623 27 44 0.366 3.234 2.473 0.549 2.166 27 48 0.347 3.253 2.473 0.559 2.205 28 0 0.369 3.244 3.086 0.002 0.006 28 2 0.329 3.284 2.523 0.435 1.717 28 4 0.332 3.281 2.496 0.493 1.944 28 20 0.304 3.309 1.575 1.321 5.209 28 24 0.270 3.343 1.292 1.868 7.367 28 44 0.186 3.427 0.596 2.722 10.735 28 48 0.162 3.451 0.509 2.846 11.224 29 0 0.375 3.239 3.102 0.001 0.006 29 2 0.366 3.248 3.117 0.009 0.034 29 4 0.377 3.237 3.099 0.023 0.089 29 20 0.380 3.234 3.092 0.032 0.125 29 24 0.379 3.235 3.058 0.039 0.154 29 44 0.374 3.240 3.013 0.053 0.209 29 48 0.373 3.241 2.950 0.059 0.233

Example 41 Production of 2-Methyl-1-butyl-COFA Ester by Lipase-Catalyzed Reaction of 2-Methyl-1-butanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.5), 2-methyl-1-butanol, lipase (Lipolase® 100 L (Novozymes), Lipozyme® CALB L (Novozymes), Rhizopus arrhizus lipase (SigmaAldrich), and Candida cylindracea lipase (SigmaAldrich) and corn oil fatty acids prepared from corn oil (Table 36) were stirred at 30° C., and samples were withdrawn while stirring from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for 2-methyl-1-butanol and 2-methyl-1-butyl esters of corn oil fatty acids (MeBO-COFA) (Table 37).

TABLE 36 Reaction conditions for conversion of 2-methyl-1-butanol (MeBOH) to 2-methyl-1-butyl esters of corn oil fatty acids (MeBO-COFA) 2-methyl- MES buffer 1-butanol COFA lipase Reaction (0.2M) (g) (g) (g) lipase (ppm) 30 46.27 3.60 14.48 Lipolase ® 10 100L 31 46.14 3.60 14.48 Lipozyme ® 10 CALB L 32 46.12 3.60 14.47 R. arrhizus 10 33 46.11 3.49 14.47 C. cylindracea 10 34 46.18 3.60 14.47 no lipase 0

TABLE 37 Weights of 2-methyl-1-butanol (MeBOH) and 2-methyl- 1-butyl esters of corn oil fatty acids (MeBO-COFA) present in the aqueous fraction (AQ) and organic fraction (ORG) for reactions described in Table 36 MeBOH MeBO- total total from MeBO- COFA reac- time MeBOH MeBOH MeBOH COFA (g) (g) tion (h) (g) (AQ) (g) (ORG) (g) (ORG) (ORG) (ORG) 30 0 0.000 3.603 3.103 0.002 0.008 30 2 0.009 3.593 2.919 0.630 2.484 30 4 0.058 3.545 2.766 0.673 2.653 30 20 0.005 3.598 2.041 1.331 5.250 30 24 0.029 3.574 1.967 1.418 5.594 30 44 0.017 3.585 1.218 2.174 8.577 30 48 0.008 3.595 1.099 2.085 8.224 31 0 0.000 3.595 3.129 0.003 0.010 31 2 0.003 3.592 2.665 0.692 2.730 31 4 0.012 3.583 2.510 0.839 3.308 31 20 0.001 3.594 1.408 1.932 7.622 31 24 0.005 3.590 1.293 2.082 8.214 31 44 0.006 3.589 0.970 2.437 9.612 31 48 0.007 3.588 0.918 2.495 9.840 32 0 0.000 3.597 3.100 0.003 0.011 32 2 0.017 3.580 2.855 0.588 2.321 32 4 0.000 3.597 2.783 0.675 2.664 32 20 0.000 3.597 2.392 1.027 4.051 32 24 0.000 3.597 2.337 1.081 4.266 32 44 0.001 3.596 2.209 1.191 4.697 32 48 0.000 3.597 2.174 1.216 4.798 33 0 0.000 3.597 3.093 0.002 0.008 33 2 0.001 3.596 1.756 1.398 5.514 33 4 0.003 3.594 2.116 1.026 4.046 33 20 0.027 3.570 0.607 2.865 11.302 33 24 0.000 3.597 0.429 3.097 12.216 33 44 0.007 3.590 0.205 3.345 13.194 33 48 0.003 3.594 0.202 3.353 13.228 34 0 0.000 3.485 3.014 0.003 0.011 34 2 0.000 3.485 2.991 0.021 0.083 34 4 0.000 3.485 3.020 0.012 0.046 34 20 0.000 3.485 2.970 0.029 0.115 34 24 0.002 3.483 2.949 0.037 0.148 34 44 0.000 3.485 2.912 0.047 0.185 34 48 0.000 3.485 2.909 0.051 0.200

Example 42 Production of Isopropyl-COFA Ester by Lipase-Catalyzed Reaction of Isopropanol and Corn Oil Fatty Acids (COFA)

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (0.20 M, pH 5.5), isopropanol (2-propanol), lipase (Lipolase® 100 L (Novozymes), Lipozyme® CALB L (Novozymes), Rhizopus arrhizus lipase (SigmaAldrich), and Candida cylindracea lipase (SigmaAldrich) and corn oil fatty acids prepared from corn oil (Table 38) were stirred at 30° C., and samples were withdrawn while stirring from each reaction mixture at predetermined times, immediately centrifuged, and the aqueous and organic layers separated and analyzed for isopropanol and isopropyl esters of corn oil fatty acids (i-PrO-COFA) (Table 39).

TABLE 38 Reaction conditions for conversion of isopropanol (i-PrOH) to isopropyl esters of corn oil fatty acids (i-PrO-COFA) MES buffer isopropanol COFA lipase Reaction (0.2M) (g) (g) (g) lipase (ppm) 35 46.14 3.60 14.48 Lipozyme ® 10 CALB L 36 46.11 3.49 14.47 C. 10 cylindracea 37 46.18 3.60 14.47 no lipase 0

TABLE 39 Weights of isopropanol (i-PrOH) and isopropyl esters of corn oil fatty acids (i-PrO-COFA) present in the organic fraction (ORG) for reactions described in Table 38 i-PrOH from i-PrO- i-PRO-COFA COFA reaction time (h) (g) (ORG) (g) (ORG) 35 0 0.001 0.00 35 2 0.013 0.07 35 4 0.038 0.20 35 20 0.132 0.71 35 24 0.177 0.94 35 44 0.291 1.55 35 48 0.301 1.61 36 0 0.001 0.01 36 2 0.051 0.27 36 4 0.163 0.87 36 20 0.532 2.84 36 24 0.652 3.48 36 44 0.916 4.89 36 48 0.959 5.12 37 0 0.001 0.01 37 2 0.001 0.01 37 4 0.003 0.02 37 20 0.009 0.05 37 24 0.011 0.06 37 44 0.016 0.09 37 48 0.023 0.12

Example 43 Comparison of Partition Coefficients for Isobutanol between Water and Extractant

Aqueous solutions of isobutanol (30 g/L) were mixed with corn oil fatty acids (COFA), or oleic acid or corn oil triglycerides, and their measured partition coefficients reported in the table relative to the measured partition coefficient for oleyl alcohol. Results are shown in Table 40.

TABLE 40 Relative partition coefficients for isobutanol (30 g/L) between water and extractant isobutanol partition coefficient, extractant relative to oleyl alcohol oleyl alcohol 100%  corn oil fatty acids 91% corn oil fatty acid isobutyl esters 43% corn oil triglycerides 10%

Example 44 Production of Corn Oil Fatty Acids

A five-liter (5L) round bottom flask equipped with a mechanical stirrer, thermocouple, heating mantle, condenser and nitrogen tee was charged with 750 g of crude corn oil (non-food grade, recovered from an ethanol fermentation facility), 2112 g of water and 285 g of 50% sodium hydroxide solution. Mixture was heated to 90° C. and held for two hours, during which time it became a single thick, emulsion-like single phase. At the end of this time, TLC shows no remaining corn oil in the mixture. The mixture was then cooled to 74° C. and 900 g of 25% sulfuric acid was added to acidify the mixture. It was then cooled to 50° C. and the aqueous layer was drained. The oil layer was washed twice with 1500 mL of 40° C. water and then once with 1 liter of saturated brine. It was dried over magnesium sulfate and filtered through Celite. Yield was 610 g of clear red oil. Titration for free fatty acids via AOCS method Ca 5a-40 shows a fatty acid content of 95% expressed as oleic acid. A sample was silanized by reacting 104 mg with 100 uL of N-methyl-N-(trimethylsilyl)trifluoroacetamide in 1 mL of dry pyridine. Gas chromatography-mass spectrometry (GCMS) analysis of the silanized product shows the presence of the TMS derivatives of the 16:0, 18:2, 18:1, 18:0, and 20:0 acids.

Example 45 Chemical Synthesis of FABE

A 3 L flask was equipped with a mechanical stirrer, thermocouple, nitrogen inlet, heating mantle and a condenser. The flask was charged with COFA (595 g) (prepared as in Example 44), isobutanol (595 g), and sulfuric acid (12 g). The mixture was refluxed for 1.5 hours at which time the condenser was removed and replaced with a still head. Distillate was collected over three hours with an initial head temperature of 90° C. and a final head temperature of 105° C. The mixture was then cooled to room temperature and 500 mL of DI water was added. The layers were separated and the organic layer was washed five times with 500 mL of DI water. It was then washed once with 500 mL of a 10% calcium chloride solution followed by six washings with 500 mL of DI water. The oil was then dried over magnesium sulfate and filtered through a bed of Celite yielding 601 g of a clear red oil. GC analysis shows the presence of 0.36 wt % of isobutanol. GC/MS analysis shows the presence of isobutyl palmitate, isobutyl stearate, isobutyl oleate, isobutyl linoleate, and isobutyl linolenate.

Example 46 Recovery of Butanol Using an Inorganic Acid Catalyst

A 1 liter round bottom flask with magnetic stirring and a 12″ column packed with Rasching rings topped with a still head and nitrogen inlet was used. The flask was charged with 254 g FABE synthesized as in Example 45, 255 g COFA, 100 mL water, and 5 g sulfuric acid, and heated to a pot temperature of 93° C. Head temperature was equilibrated at 89.7° C. The first cut was collected with a reflux ratio that maintained the head temperature between 89 and 94° C.

The reaction was cooled and sat at room temperature for three days. GC analysis of the pot shows a total of 1 g of isobutanol in the pot. The distillation was restarted and three more cuts, each of 25 mL, were collected. One hundred (100) mL of water was added to the pot after collecting cut #2. Four cuts were collected and analyzed with the results shown in Table 41.

GC analysis was done using a Hewlett Packard 6890 GC using a 30 m FFAP column. Samples were dissolved in isopropanol and 1-pentanol was added as an internal standard. Standard curves were made for isobutanol, isobutyl palmitate, isobutyl stearate, isobutyl oleate, isobutyl linoleate, isobutyl linolenate, isobutyl arachidate, palmitic acid, stearic acid, oleic acid, linoleic acid and linolenic acid. FABE content is reported as the sum of the butyl esters and COFA content as the sum of the fatty acids.

TABLE 41 Composition analysis of cuts collected i-BuOH wt of i- mg/ml mL BuOH Cut 1 60 43 2.6 Cut 2 41 23.4 1 Cut 3 29 24.2 0.7 Cut 4 30 27 0.8 Total 117.6 5.1

Example 47 Recovery of Butanol Using an Organic Acid Catalyst

A 1 liter 3 neck round bottom flask equipped with magnetic stirrer, thermocouple, addition funnel and still head was used. The flask charged with 100 g FABE synthesized as in Example 45, 100 g COFA, 5 g p-toluenesulfonic acid, and 25 mL water. Isobutanol analysis of initial pot shows 1.1 g of isobutanol present (contaminant in FABE). The pot was heated to 125° C. When the pot reached 116° C. head temperature was 96° C., and 125 mL water was added over 2.5 hours. Six cuts were collected over the time that the water was added and they were analyzed by GC as in Example 46. Results are provided in Table 42.

TABLE 42 Composition analysis of cuts collected mL of mg/ml g i- pot head water i-BuOH BuOH cut temp temp added in cut mL in cut #1 116 96 25 53 13 0.7 #2 117 98 47 52 26 1.4 #3 117 99 70 37 24 0.9 #4 117 99 95 30 22 0.7 #5 117 99 125 23 31 0.7 #6 117 99 39 41 1.6 Total 5.9

Butanol analysis of the remaining still pot shows 0.9 g of free isobutanol present. The initial COFA:FABE mixture analyzed was 45 wt % FABE. The final pot analyzed was 32 wt % FABE.

Example 48 Hydrolysis of FABE with Water at High Temperature

A 1 liter autoclave was charged with FABE synthesized as in Example 45, 300 mL and 300 mL water. It was sealed and purged with nitrogen. Stirring was started and it was then heated to 250° C. over 45 minutes and samples were removed every hour after reaching temperature. The samples were analyzed by GC as in Example 46. The oil phase samples showed the compositions as a function of time shown in Table 43.

TABLE 43 Composition of organic phase of samples wt % wt % wt % Time i-BuOH FABE COFA 0 0 97 2 1 3 76 18 2 6 50 41 3 7 36 45 4 7 34 48 5 7 35 51

Example 49 Hydrolysis of FABE with Dilute Acid at High Temperature

A 1 liter autoclave was charged with 450 g of a 75/25 mixture of FABE synthesized as in Example 45 and COFA and with 150 g of 2% sulfuric acid. It was sealed and purged with nitrogen. Stirring was started and it was then heated to 225° C. over 45 minutes and samples were removed every hour after reaching temperature. The samples were analyzed by GC as in Example 46. The oil phase samples showed the compositions as a function of time shown in Table 44.

TABLE 44 Composition analysis of cuts collected Time wt % wt % wt % (h) i-BuOH FABE COFA 0 2.2 61.8 34.1 1 3.8 47.8 42.0 2 5.2 38.4 48.2 3 5.3 38.4 53.5 4 5.1 33.4 48.2 5 5.1 31.9 43.3 6 5.5 35.2 51.7

Example 50 Hydrolysis of FABE with Sulfuric Acid in Solvent at 100° C.

A solution of 5 g FABE synthesized as in Example 45, 5 g of 25% sulfuric acid, and 60 g of diethyleneglycol dimethyl ether was prepared. Ten (10) g of the solution was added to each of five vials which were then sealed. All of the vials were heated to 100° C. and one vial was removed from the heater and analyzed every hour. The resulting compositions were determined by GC (as described in Example 46) and are reported in Table 45.

TABLE 45 Composition analysis of cuts collected Time wt % wt % wt % (h) i-BuOH FABE COFA 0 0.11 5.74 0 1 1.1 1.72 1.23 2 1.32 0.96 1.77 3 1.35 0.76 1.8 4 1.38 0.7 1.81 5 1.37 0.72 1.82 15 1.37 0.84 2.12

Example 51 Hydrolysis of FABE by Reactive Distillation

A 12 liter flask was equipped with an insulated 2″×30″ column topped with a feed inlet and a still head. The column was randomly packed with one liter of Pro-pak® (316 SS 0.16″) still packing and 500 g of Amberlyst® 36 solid acid catalyst (Dow). The flask was charged with 6 liters of water and brought to a boil. The heat was controlled to have a water distillation rate of about 1.8 mL/min. FABE synthesized as per the method described in Example 45 was added to the top of the column at a rate of 2 g/min. The feed was continued for a total of 60 minutes. The distillation was continued for another 30 minutes. A total of 194 g of distillate was collected which contained 2.1 g of isobutanol. Based on the amount of FABE fed this represents a 9% conversion of FABE to butanol.

Example 52 Hydrolysis of FABE by Counter Current Steam

The apparatus as described in example 50 was modified by the addition of heat tape wrapped around the still column. The temperature in the upper half of the column was adjusted to 115° C. and the temperature in the lower half of the column was adjusted to 104° C. The pot was brought to a boil and the pot heat was adjusted until water was distilling at a rate of 1.5-2 mL/min. FABE (346 g) synthesized as per the method described in Example 45 was fed to the top of the packed column over a period of three hours while the distillation continued. After the feed period the distillation was continued for another 90 minutes. A total of 486 g of distillate was collected that contained 30.1 g of isobutanol. This represents a conversion of FABE to isobutanol of 39%.

Example 53 Hydrolysis Catalyzed by a Water Insoluble Organic Acid

A one liter 3 n round bottom flask equipped with an oil bath, mechanical stirrer, nitrogen inlet, subsurface water inlet, and a still head was charged with 150 g of FABE, 50 g water, and 5 g dodecylbenzene sulfonic acid. An oil bath was heated to 95-100° C. and a slow nitrogen sweep started. Distillate cuts were collected every half hour for a total of five hours. After three hours, water was fed to the still pot at a rate of 15 mL/hr. Distillate cuts were analyzed for isobutanol content by the GC method described in Example 46 and the results are shown in Table 46. Approximately 44% of the isobutanol contained in the FABE was collected over five hours.

TABLE 46 Sample Cumulative i-BuOH collected (g) 1 0.80 2 1.47 3 2.46 4 3.99 5 5.71 6 7.75 7 9.16 8 10.33 9 13.76 10 14.37

Example 54 Hydrolysis Catalyzed by Solid Acid Catalyst

A one liter 3 n round bottom flask equipped with an oil bath, mechanical stirrer, subsurface nitrogen inlet, subsurface water inlet, and a still head was charged with 150 g of FABE and 50 g of dry Amberlyst 15 solid acid catalyst. The flask was heated to 110° C. with the oil bath and water was added via a syringe pump at a rate of 15 mL/hr. Distillation fractions were collected every half hour for a total of five hours. The fractions were analyzed for isobutanol content by the GC method described in Example 46 and the results are shown in Table 47. Approximately 44% of the theoretical amount of isobutanol contained in the FABE was collected over five hours.

TABLE 47 Sample Cumulative i-BuOH collected (g) 1 0.3 2 0.9 3 2.3 4 3.4 5 4.4 6 5.5 7 6.3 8 6.9 9 7.4 10 8.0

Example 55 Hydrolysis Catalyzed by Water Soluble Organic Acid Catalyst

A one liter flask with mechanical stirrer, subsurface nitrogen inlet, subsurface water inlet, and a still head was charged with 200 g of FABE and 10 g of p-toluenesulfonic acid. The flask was stirred and heated to 110° C. with an oil bath at which time water was added at a rate of 20 mL/hr via a syringe pump. Still fractions were collected every half hour for a total of three hours. The fractions were analyzed for isobutanol content by the GC method described in Example 46 and the results are shown in Table 48. Approximately 30% of the theoretical amount of isobutanol contained in the FABE was collected over five hours.

TABLE 48 Fraction Cumulative amount of isobutanol 1 1.0 2 4.0 3 7.2 4 9.5 5 11.8 6 13.4

Example 56 Hydrolysis of Solvent Phases from Fermentation A. Solvent Phase 1

The solvent phase from the fermentation shown in Example 17 was analyzed by the GC method shown in Example 46 and the results are shown in Table 49. The analysis shows primarily FABE and fatty acids with a small amount of material with a retention time consistent with FAEE. Analysis of just the butyl esters and acids shows a ratio of 62% FABE and 39% fatty acids.

The solvent phase (1.25 liters, 1090 g) and 1.25 liters of water were charged to a one gallon autoclave. The autoclave was sealed and heated to 250° C. and held at temperature for four hours. The autoclave was then cooled and opened, giving an emulsion. The mixture was filtered through a bed of Celite and the layers were separated. The organic layer was washed three times with one liter of water. The sample was then heated to 50° C. and purged with nitrogen for six hours. GC analysis shows no i-BuOH and a ratio of 33% FABE and 67% fatty acids. An amber oil (993.9 g) was obtained. A detailed compositional analysis of the original solvent phase from fermentation Example 17 and the post-hydrolysis solvent phase is shown in Table 50.

B. Solvent Phase 2

The solvent phase from the fermentation shown in Example 18 was analyzed by the GC method shown in Example 46 and the results are shown in Table 49. The analysis shows primarily FABE and fatty acids with a small amount of material with a retention time consistent with FAEE. Analysis of just the butyl esters and acids shows a ratio of 45% FABE and 55% fatty acids.

The solvent (1.25 liters, 1100 g) and 1.25 liters of water charged to a one gallon autoclave. The autoclave was sealed and heated to 250° C. and held at temperature for four hours. The autoclave was then cooled and opened, giving an emulsion. The mixture was filtered through a bed of Celite and the layers were separated. The organic layer was washed three times with one liter of water. The sample was then heated to 50° C. and purged with nitrogen for six hours. GC analysis shows no i-BuOH and a ratio of 28% FABE and 72% fatty acids. An amber oil (720.5 g) was obtained.

TABLE 49 Pre-hydrolysis Post-hydrolysis FABE Fatty FABE Fatty Sample (%) Acid (%) (%) Acid (%) Solvent 62 39 33 67 Phase 1 Solvent 45 55 28 72 Phase 2

TABLE 50 Solvent Post Hydrolysis Phase 1 (wt %) Composition (wt %) Isobutyl palmitate 7.28 4.24 Isobutyl stearate 3.41 2.25 Isobutyl oleate 13.92 7.69 Isobutyl linoleate 33.09 17.73 Isobutyl linolenate 2.78 Palmitic acid 3.79 7.3 Stearic acid 2.58 4.07 Oleic acid 9.14 16.61 Linoleic acid 19.06 33.54 Linolenic acid 2.3 2.65

Example 57 Recovery of Product Alcohol—Hydrolysis using a Lipase Catalyst

FABE was synthesized from corn oil fatty acid as per the method described in Example 44. Novozyme 435 (Novo 435, Candida antarctica lipase B, immobilized on an acrylic resin) was purchased from Sigma Aldrich (St. Louis, Mo.). Candida antarctica Lipase B was purchased from Novozymes (Franklinton, N.C.). t-BuOH, acetone, ethanol, methanol, and glycerol were all purchased from Sigma Aldrich (St. Louis, Mo.). For gas chromatography (GC) analysis, the gas chromatograph used was Hewlett Packard 5890 Series II GC chromatogram and methyl pentadecanoate was used as an internal standard.

A. Atmospheric Pressure, 40° C.

To a mixture of 2 mL FABE and 5 mL water was added 40 mg Novozyme 435, and the reaction mixture was placed in a 20 mL vial and incubated at 40° C. in a rotary shaker (300 rpm). The reaction mixture was analyzed using GC during 24 h of the reaction, to generate the following % conversion profile given in Table 51:

TABLE 51 % Conversion Profile for Example 57A Reaction time (h) % FABE conversion 0 0 1 6.7 1.5 10.5 2 15.1 4 17.0 6 17.4 8 17.7 24 18.2

B. Atmospheric Pressure, 40° C., 65° C. And 80° C., No Organic Solvent

Together with part A of this example, these data show how equilibrium changes with temperature

To a mixture of 1 mL FABE and 2 mL water was added 20 mg Novozyme 435 and the reaction mixture was rotated at 40° C. for 45 h in a 6 mL septum-capped vial. The reaction mixture was analyzed using GC to reveal 18.2% conversion of FABE at equilibrium.

To a mixture of 1 g FABE and 2 mL water was added 20 mg Novozyme 435, and the reaction mixture was rotated at 65° C. for 42 h in a 6 mL septum-capped vial. The reaction mixture was analyzed using GC to reveal 19.8% conversion of FABE at equilibrium.

To a mixture of 1 g FABE and 2 mL water was added 20 mg Novozyme 435, and the reaction mixture was rotated at 80° C. for 42 h in a 6 mL septum-capped vial. The reaction mixture was analyzed using GC to reveal 21.4% conversion of FABE at equilibrium.

C. Example Showing the Effect of Organic Solvent (t-BuOH) on the Equilibrium

To three reaction mixtures containing 0.25 mL FABE, 0.75 mL t-BuOH, and 0.1-0.3 mL water was added 20 mg Novozyme 435, and the mixtures, in 6 mL septum-capped vials, were left rotating at 40° C. overnight, at which point they had reached equilibrium. The reaction mixtures were analyzed using GC after 24 h of the reaction, to generate 77-82% FABE conversions given in Table 52. Replacing t-BuOH with 3-Me-3-pentanol under similar reaction conditions gave FABE hydrolysis yields of 70-80%.

TABLE 52 % Conversion Profile for Example 57C Novozyme % FABE Reaction mixture 435 loading conversion 0.75 mL t-BuOH, 0.25 mL 20 mg 77% FABE, 0.1 g H₂O 0.75 mL t-BuOH, 0.25 mL 20 mg 81% FABE, 0.2 g H₂O 0.75 mL t-BuOH, 0.25 mL 20 mg 82% FABE, 0.3 g H₂O

D. Acetone as Solvent

To three reaction mixtures containing 0.25 mL FABE, 0.75 mL acetone, and 0.1-0.3 mL water was added 20 mg Novozyme 435, and the mixtures, in 6 mL septum-capped vials, were left rotating at 40° C. overnight, at which point they had reached equilibrium. The reaction mixtures were analyzed using GC after 24 h of the reaction, to show 71-78% FABE conversions given in Table 53.

TABLE 53 % Conversion Profile for Example 57D Novozyme % FABE Reaction mixture 435 loading conversion 0.75 mL acetone, 0.25 mL 20 mg 71% FABE, 0.1 g H₂O 0.75 mL acetone, 0.25 mL 20 mg 74% FABE, 0.2 g H₂O 0.75 mL acetone, 0.25 mL 20 mg 78% FABE, 0.3 g H₂O E. Example Showing the Effect of Removing i-BuOH During Hydrolysis on FABE Conversion—Nitrogen Purge at Atmospheric Pressure

A 25 mL round bottom flask was charged with 2 mL FABE, 5 mL water, and 40 mg Novozyme 435. The reaction mixture was heated to 95° C., and the i-BuOH that was forming in the reaction was removed by bubbling nitrogen through the reaction mixture. Samples were taken from the mixture during the reaction, and the organic phase was analyzed using GC. Conversion of 94% was achieved after 6 h as shown in Table 54:

TABLE 54 FABE Conversion Profile for Example 57E Reaction time (h) Mole % COFA in COFA + FABE 0 1 1 62 2 76 3 86 4 90 6 94 F. Example Showing the Effect of Removing i-BuOH During Hydrolysis on the Conversion-Vacuum Distillation

A 25 mL round bottom flask was charged with 3 mL FABE, 7.5 mL of water, and 60 mg Novozyme 435. The flask was attached to a vacuum distillation apparatus, and the pressure was set to 91 mm Hg. The reaction mixture was then heated to 74° C., and the i-BuOH that was forming in the reaction was distilled off. Samples were taken from the mixture during the reaction, and the organic phase was analyzed using GC. Conversion of 91% was achieved after 10 h as shown in Table 55.

TABLE 55 % Conversion Profile for Example 57F Reaction time (h) % FABE conversion 0 0 1 16 2 37 3 57 5 72 7 83 10 91 G. Example Showing the Effect of Removing i-BuOH During Hydrolysis on the Conversion-Vacuum Distillation Example-Varying FABE/COFA Starting Ratio: 23% FABE:77% COFA v/v

A 25 mL round bottom flask was charged with 0.69 mL FABE, 2.31 mL COFA, 7.5 mL water, and 60 mg Novozyme 435. The flask was attached to a vacuum distillation apparatus, and the pressure was set to 91 mm Hg. The reaction mixture was then heated to 74° C., and the i-BuOH that was forming in the reaction was distilled off. Samples were taken from the mixture during the reaction, and the organic phase was analyzed using GC. Conversion of 98% was achieved after 10 h as shown in Table 56.

TABLE 56 FABE Conversion Profile for Example 57G Reaction time (h) Mole % COFA in COFA + FABE 0 77 1 83 2 86 3 90 4 92 6 93 7 96 10 98 H. Example Showing the Effect of Removing i-BuOH During Hydrolysis on the Conversion-Vacuum Distillation Example-Varying FABE/COFA Starting Ratio: 70% FABE:30% COFA v/v

A 25 mL round bottom flask was charged with 2.1 mL FABE, 0.9 mL COFA, 7.5 mL water, and 60 mg Novozyme 435. The flask was attached to a vacuum distillation apparatus, and the pressure was set to 91 mm Hg. The reaction mixture was then heated to 74° C., and the i-BuOH that was forming in the reaction was distilled off. Samples were taken from the mixture during the reaction, and the organic phase was analyzed using GC. Conversion of 96% was achieved after 10 h as shown in Table 57:

TABLE 57 FABE Conversion Profile for Example 57H Reaction time (h) Mole % COFA in COFA + FABE 0 30 1 52 2 64 5 84 7 89 10 96

I. Example Showing the Free Cal B Enzyme in FABE Hydrolysis Under Vacuum Distillation Conditions

Two round bottom flasks were charged with 3 mL (2.7 g) FABE and 7.5 mL H₂O each. To one mixture was added 5.9 mg Candida antarctica Lipase B, and to the other was added 0.59 mg enzyme. The reaction flasks were separately connected to the distillation apparatus and exposed to pressure of 91 mm Hg. The reaction mixtures were heated to 65-68° C. Samples were taken from the reaction mixtures over a ten-hour period, and analyzed using gas chromatography. The final FABE conversions were 96 and 78%, respectively. The experiments show that reducing the amount of enzyme concentration by a factor of ten reduces the rate and conversion by 3× and 18%, respectively. The results are shown in Table 58.

TABLE 58 FABE Conversion Profile for Example 57I Mole % COFA in COFA + Mole % COFA in COFA + Reaction FABE with 5.9 mg CALB/ FABE with 0.59 mg CALB/ time (h) 2.7 g FABE 2.7 g FABE 0 0 0 1 44 21 2 62 31 6 89 61 10 96 78

Example 58 Recovery of Product Alcohol—Transesterification

FABE was synthesized from corn oil fatty acid as per the method described in Example 44; Novozyme 435 (Candida antarctica lipase B, immobilized on an acrylic resin) was purchased from Sigma Aldrich (St. Louis, Mo.). Candida antarctica Lipase B was purchased from Novozymes (Franklinton, N.C.). t-BuOH, acetone, ethanol, methanol, and glycerol were all purchased from Sigma Aldrich (St. Louis, Mo.). For GC analysis, the gas chromatograph used was Hewlett Packard 5890 Series II GC chromatogram and methyl pentadecanoate was used as an internal standard.

Testing Lipases—FABE to FAME

Reagents used were t-BuOH (Aldrich); MeOH (Aldrich); Novozyme 435 (Aldrich); PS30 (Burkholderia cepacia, Amano Enzymes, Inc, Elgin, Ill.); Lipolase® 100T (Thermomyces lanuginosa, immobilized on silica, Novozymes, Franklinton, N.C.); Lipolase® 100L (Thermomyces lanuginosa, Novozymes, Franklinton, N.C.); Lipozyme® TLIM (immobilized Thermomyces lanuginosa, Novozymes, Franklinton, N.C.); Lipoclean® 2000T (immobilized mixture of lipases; Novozymes, Franklinton, N.C.); NZL-103-LYO (Lipase from Rhizomucor miehi, Novozymes, Franklinton, N.C. To a 6 mL vial was added 500 mg FABE (1.48 mmol), 400 μL t-BuOH, 60 μL MeOH (1.48 mmol), 3 μL water, and 2.5 mg lipase (see Table 57). The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed the conversions from 9-56%. Results are shown in Table 59.

TABLE 59 Equilibrium concentrations [mg/mL] and % conversion of FABE→FAME using different lipases FABE COFA i-BuOH % Lipase (mg/mL) (mg/mL) (mg/mL) conversion PS30 471 2.48 11.2 9.73% NOVOZYME 435 224 16.8 63.7 56.30% LTLIM 266 15.9 67.7 53.50% L100T 455 1.8 8.9 8.80% 2000T 452 1.8 9.1 8.31% NZL-103-LYO 429 3.94 15.3 13.90%

B. FABE to FAME Transformation—Optimizing the Amount of Methanol

To a 6 mL vial was added 500 mg FABE (1.48 mmol), 400 μL t-BuOH, 60-240 μL MeOH (1.48-5.92 mmol), 3 μL water, and 2.5 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed the conversions from 53-73% as shown in Table 60.

TABLE 60 % Conversion Profile for Example 58B MeOH FABE COFA i-BuOH % eq's (mg/mL) (mg/mL) (mg/mL) conversion 1.2 232 2.4 66.9 56.64 1.4 168 2.4 70.4 65.50 1.6 167 0 72.1 66.17 1.8 184 0 80.3 66.41 2.0 131 0 72.4 71.46 2.2 134 1.2 81 73.25 2.4 136 0 80 72.71 2.6 161 0 78 68.70 2.8 168 0 73 66.31 3.0 155 0 74 68.38 3.2 180 0 73 64.75 3.4 161 0 78 68.70 3.6 192 0 66 60.89 3.8 236 0 63 54.74 4.0 243 0 61 53.21

C. Optimizing the Amount of Enzyme—FABE to FAME

To a 6 mL vial was added 500 mg FABE (1.48 mmol), 400 μL t-BuOH, 132 μL MeOH (3.26 mmol), and 5-25 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed the conversions from 76-79% as shown in Table 61.

TABLE 61 % Conversion Profile for Example 58C FABE COFA i-BuOH % Novozyme 435 (mg) (mg/mL) (mg/mL) (mg/mL) conversion 5 mg 129.4 0 88 75.49 7.5 mg 119.3 0 89.2 77.21 10 mg 110.9 0 89 78.43 12.5 mg 109.2 0 84.9 77.89 15 mg 112.4 0 86.1 77.63 17.5 mg 108.4 0 87.4 78.51 20 mg 115.6 0 91.8 78.25 22.5 mg 108.6 0 87.7 78.53 25 mg 111.6 0 89 78.32 D. Minimizing the Amount of Solvent (t-BuOH)—FABE to FAME

To a 6 mL vial was added 500 mg FABE (1.48 mmol), 0-300 μL t-BuOH, 132 μL MeOH (3.26 mmol), and 10 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed the conversions from 30-81% as shown in Table 62.

TABLE 62 % Conversion Profile for Example 58D % FAME FABE COFA i-BuOH conver- (mg/ Amount (mg/mL) (mg/mL) (mg/mL) sion mL) 300 μL t-BuOH 94.3 0 83 79.95 295 200 μL t-BuOH 94.1 0 83.2 80.02 295 100 μL t-BuOH 91.7 0 84.2 80.62 300  50 μL t-BuOH 92.9 0 81 79.80 290.8 <50 μL t-BuOH 137 0 70.5 69.98 249.4 no t-BuOH 322.7 1.39 30.2 29.77 98.1

E. Minimization of the Amount of Solvent β-Me-3-Pentanol)—FABE to FAME

To a 6 mL vial was added 500 mg FABE (1.48 mmol), 0-300 μL 3-Me-3-pentanol, 132 μL MeOH (3.26 mmol), and 10 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed the conversions from 30-78% as shown in Table 63.

TABLE 63 % Conversion Profile for Example 58E % FAME FABE COFA i-BuOH Conver- (mg/ Amount (mg/mL) (mg/mL) (mg/mL) sion mL)  0.3 mL 3M3P 115.6 3.75 81.4 76.13 296  0.2 mL 3M3P 106.3 3.13 80 77.32 294  0.1 mL 3M3P 104.8 2.36 80.8 77.74 296 0.05 mL 3M3P 102.9 2.3 79.6 77.80 295 soak 3M3P 102.5 2.4 79.9 77.93 296 no 3M3P 322.7 1.39 30.2 29.77 98.1 F. Conversion of FABE to FAME without Solvent

To a mixture of FABE (500 mg, 1.48 mmol) and methanol (0.13 μL, 3.25 mmol) was added 40 mg Novozyme 435, and the reaction mixture was stirred at 40° C. overnight. The mixture was then filtered and analyzed by GC to reveal 76% conversion.

G. Enzyme Recycle—FABE to FAME

To a 6 mL vial was added 500 mg FABE (1.48 mmol), 400 μL t-BuOH, 132 μL MeOH (3.26 mmol), and 10 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. After that time, the reaction mixture was filtered and analyzed for conversion using GC, and the filter cake containing the immobilized enzyme, was used for another conversion of FABE to FAME. The process was repeated ten times (Table 64). The experiment shows that it is possible to recycle the enzyme up to ten times without the loss in conversion in the overnight reaction.

TABLE 64 % Conversion Profile for Enzyme Recycle in Example 58G Concentrations are in mg/mL % FABE to Conver- FAME FABE COFA i-BuOH sion FAME 1st  115.8 5.29 82.1 76.26 298.1  2nd 124 5.36 82.7 75.13 293.2 3rd 112 4.82 85 77.47 303.1 4th 111 9.06 85.1 77.64 306.3 5th 99.4 5.1 82.1 78.91 284.5 6th 98.2 6 81.2 78.93 283.8 7th 115.6 6.8 78.9 75.56 262.7 8th 114.8 6.5 77.6 75.38 257.2 9th 99 5.7 78 78.12 241 10th  109 8.6 73.7 75.39 226.7

H. Conversion of FABE to FAEE

To 6 mL septum-capped vials were added 0.8 mL FABE (2.08 mmol) and 0.2 mL EtOH (3.43 mmol), forming a single phase. No enzyme or 20 mg Novozyme 435 was added to the vials. The vials were then incubated at 25° C. and 40° C. in an incubator shaker (300 rpm) for 17 h after which the solution was analyzed by gas chromatography, giving the contents and percent conversion of FABE to FAEE shown in Table 65.

TABLE 65 FABE i-BuOH COFA % Sample (mg/mL) (mg/mL) (mg/mL) Conversion EtOH/FABE + 93.2 38.5 0 41.6 enzyme, 25° C. EtOH/FABE, no 159.6 3.5 0.75 0 enzyme, 25° C. EtOH/FABE + 90 35.7 0 43.3 enzyme, 40° C. EtOH/FABE, no 158.7 3.1 0.75 0 enzyme, 40° C.

Example 59 Glycerolysis of FABE

To a septum-capped 6 mL vial was added 0.75 mL t-BuOH, 0.25 mL FABE, 0.1 mL (0.126 g) glycerol+4 μL H₂O, enzyme 20 mg each, forming a single phase. The reactions were incubated with various lipases at 40° C. on a rotary shaker at 300 rpm. After 20 h, the samples were analyzed by gas chromatography, giving the contents shown in Table 66. A comparison of the COFA and FABE contents indicates that the products are i-BuOH and a mixture of COFA and acyl glycerol (˜64% acyl glycerol/36% COFA on molar basis).

TABLE 66 Percent conversion of FABE to a mixture of COFA and acyl glycerol Percent FABE COFA i-BuOH conversion Lipase (mg/mL) (mg/mL) (mg/mL) of FABE Amano PS-30 powder 73 43 32 64% IM-20, powder 162.4 10.2 10.9 19% Lipolase ® 100T 190 0 4 ~0% immobilized Novozyme 435 73 39.5 30.8 64% immobilized Lipozyme ® TL IM 101.7 29 26.1 49% immobilized Lipoclean ® 2000T 200.9 0 3.9 ~0% immobilized

A. Dependence on Water and Glycerol/FABE

To 6 mL septum capped vials were added 0.75 mL t-BuOH, 0.25 mL FABE, 0.1 or 0.2 g glycerol+20 mg each of either Amano PS-30 or Novozyme 435, forming a single phase. No water was added. The reactions were incubated at 40° C. on a rotary shaker at 300 rpm. After 20 h, the samples were analyzed by gas chromatography, giving the contents shown in Table 67. A comparison of the COFA and FABE contents indicates that the products are i-BuOH and primarily acyl glycerol (mostly monoglyceride). Relative to the previous example, the percent of product in the form of acyl glycerol increases with the absence of added water and with the increase in glycerol/FABE (˜91% acyl glycerol/9% COFA on molar basis with 1.6 glycerol/FABE, mole/mole and ˜95% acyl glycerol/5% COFA on molar basis with 3.2 glycerol/FABE, mole/mole). The absence of added water eliminates the enzyme activity of Amano PS-30. The Novozyme 435 which has water in the acrylic resin (˜3% w/w) to which it is immobilized is, however, still active.

TABLE 67 Percent conversion of FABE to acyl glyceride Percent FABE COFA i-BuOH conversion Lipase Glycerol (mg/mL) (mg/mL) (mg/mL) of FABE Amano 0.1 g 209 1.2 4.4 ~0% PS-30 powder Novozyme 0.1 g 84.2 10.7 28.6 58% 435, immobilized Amano 0.2 g 182 0.74 3.8 ~0% PS-30 powder Novozyme 0.2 g 61.5 7.1 30.6 ~69%  435 immobilized

B. Dependence on Enzyme Concentration

To 6 mL septum capped vials was added 0.75 mL t-BuOH, 0.25 mL FABE, 0.2 g glycerol (glycerol/FABE 3.2/1, mole/mole)+2 or 20 mg of Novozyme 435 (Novo 435). No water was added. The reactions were incubated at 40° C. on a rotary shaker at 300 rpm and the reaction was followed as a function of time by gas chromatography. The yields are indicated in Table 68. Approximately 97% of the FABE that reacted was converted to acyl glycerol (mostly monoglyceride) on a mole basis.

TABLE 68 Time % FABE conversion % FABE conversion (h) 2 mg Novo 435 20 mg Novo 435 0 0 0 0.167 13.2 0.333 38 0.5 3.37 42.9 1 10.8 59.1 2 21.9 65.5 4 31.6 67.1 6.5 32.1 7 45.7 67.1 24 64 67.3

The rate of the reaction is linear with enzyme concentration, with t_(1/2) for 2 and 20 mg of Novozyme 435 of 208 and 20 minutes, respectively. The reaction, however, reaches nearly the same yield of FABE conversion after 24 h.

These last reactions were repeated with 0.75 mL of 3-methyl-3-pentanol replacing 0.75 mL of t-BuOH. The extent of FABE hydrolysis obtained after 24 h was the same for both solvents. The advantage of 3-methyl-3-pentanol is that with a boiling point of 122° C., the i-BuOH can be distilled off first in pure form (b.p. 108° C.). The 3-methyl-3-pentanol can then be distilled off and recycled for the hydrolysis reaction, leaving in the retentate acyl glycerol, COFA, and glycerol to be recycled to the fermentation tank for reuse in the generation of FABE. Tertiary alcohols act as a solvent alone and have the advantage of not reacting with the fatty acid to form fatty acid alkyl esters in the presence of CALB.

C. Glycerolysis of FABE (FABE to COFA+Acyl Glycerol) in the Absence of Organic Cosolvent—Dependence on Glycerol Concentration

One gram (1 g) of FABE was mixed with 2 mL of 50, 70, 90, and 100% (w/w) glycerol and placed in a 6 mL septum-sealed vial in the presence of 20 mg Lipobond (Sprin Technologies, Trieste, Italy). The vial was tumbled end-over-end for 24 h at 62° C. With increasing glycerol concentration in the aqueous phase, the percent of the product in the form of acyl glycerol increases (Table 69, mostly monoglyceride). The extent of FABE conversion, however, does not show a dependence on the glycerol concentration.

TABLE 69 Condition % of COFA % of acyl glycerol (% glycerol in % of FABE in product in product aqueous phase) conversion (mole basis) (mole basis) 50 18 100 0 70 17 84 16 90 17 34 66 100 17 3 97

Example 60 Conversion of COFA to FAEE and Monoacyl Glycerol

The following examples show that COFA can be esterified with EtOH or with glycerol at high yield under mild conditions using immobilized enzyme.

Novozyme 435 (Candida antarctica lipase B, immobilized on an acrylic resin) was purchased from Sigma Aldrich (St. Louis, Mo.). Acetone, t-BuOH, ethanol, methanol, and glycerol were all purchased from Sigma Aldrich (St. Louis, Mo.). For GC analysis, the gas chromatograph used was Hewlett Packard 5890 Series II GC chromatogram and methyl pentadecanoate was used as an internal standard.

Conversion of COFA to FAEE+i-BuOH Using Ethanol

Corn oil fatty acid (COFA, 0.25 g) was dissolved in 2.0 mL EtOH forming a single phase. Twenty mg of Candida antarctica lipase B (CALB) immobilized on acrylic resin (Novozyme 435) was added (contains 1.7 mg of enzyme) and the suspension was incubated for 24 h on a rotary shaker (300 rpm) at 40° C. in a 6 mL glass vial sealed with a septum cap. The reaction went practically to completion with 98% of the COFA converted to FAEE (fatty acid ethyl ester). The GC analysis after 24 h showed 98% conversion of COFA to fatty acid ethyl ester as shown in Table 70.

TABLE 70 % Conversion Profile for Example 60A Reaction mix Novozyme 435 % Conversion of bp of EtOH = 78.1° C. loading COFA to FAEE Phases 2.0 mL EtOH + 20 mg (contains 98 1 0.25 g COFA 1.7 mg CALB) throughout Moles EtOH/ moles COFA = 38.7 B. Conversion of COFA to Monoacylglycerides (MAG)+i-BuOH Using Glycerol

Corn oil fatty acid (COFA, 0.25 g) plus 0.325 g of glycerol were dissolved in 2.0 mL acetone. There was a large upper phase in which most of the components were dissolved and a small residual glycerol-containing phase. Twenty mg of Candida antarctica lipase B (CALB) immobilized on acrylic resin (Novozyme 435) was added (contains 1.7 mg of enzyme) and the suspension was incubated for 24 h on a rotary shaker (300 rpm) at 40° C. in a 6 mL glass vial sealed with a septum cap. GC of the upper phase indicated that 87% of the COFA had been converted to acyl glyceride (expected to be mostly mono-acylglyceride). Results are shown in Table 71.

TABLE 71 % Conversion Profile for Example 60B % Conversion Reaction mix of COFA to bp of Novozyme 435 acyl glyceride acetone = 56° C. loading (mostly MAG) Phases 2.0 mL acetone + 20 mg (contains 87 Minor glycerol 0.25 g COFA + 1.7 mg CALB) phase throughout 0.325 g glycerol at 40° C. Moles glycerol/ moles COFA = 4

Example 61 Conversion of COFA to FAME

The following examples show that COFA can be esterified with MeOH, with EtOH, and with glycerol at high yield under mild conditions using immobilized lipase.

A. Conversion of COFA to FAME without Solvent

To a 6 mL vial was added 500 mg COFA (1.48 mmol), 132 μL of MeOH (3.26 mmol), and 10 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed 95% conversion.

B. Time Course Measurement of COFA to FAME Reaction

To a 6 mL vial was added 500 mg COFA (1.48 mmol), 132 μL of MeOH (3.26 mmol), and 10 mg Novozyme 435. The samples were incubated at 40° C. in an incubator/shaker and time points were taken during the reaction, and analyzed using GC. Results are shown in Table 72.

TABLE 72 COFA FAME Conversion Time [mg/mL] [mg/mL] [%] 0 min 377 0  0% 10 min 242.2 135 35% 20 min 173.6 231.8 56% 30 min 122.8 274.3 68% 1 hr 59.2 373.2 86% 2 hr 18.2 389.9 95% 3 hr 16.8 406.2 96% 4 hr 15.6 404.4 96% 7 hr 16 411.2 96%

C. Adding More MeOH to the COFA→FAME Reaction

To a 6 mL vial was added 500 mg COFA (1.48 mmol), 180, 240, 300, or 1320 μL of MeOH (4.44, 5.92, 7.41, and 14.82 mmol), and 10 mg Novozyme 435. The resulting mixture was placed in an incubator/shaker, and left at 40° C. overnight. GC analysis of the reaction mixture revealed 96-97% conversion. The results are shown in Table 73.

TABLE 73 MeOH COFA FAME % [eq] [mg/mL] [mg/mL] Conversion 3 13.26 377 96.44% 4 13.15 398.9 96.65% 5 12.12 391.8 96.85% 10 12.65 399.5 96.78%

Example 62

This example illustrated the removal of solids from stillage and extraction by desolventizer to recover fatty acids, esters, and triglycerides from the solids. During fermentation, solids are separated from whole stillage and fed to a desolventizer where they are contacted with 1.1 tons/hr of steam. The flow rates for the whole stillage wet cake (extractor feed), solvent, the extractor miscella, and extractor discharge solids are as shown in Table 74. Table values are short tons/hr.

TABLE 74 Extractor Solids from discharge whole stillage Solvent Miscella solids Fatty acids 0.099 0 0.0982 0.001 Undissolved solids 17.857 0 0.0009 17.856 Fatty acid butyl esters 2.866 0 2.837 0.0287 Hexane 0 11.02 10.467 0.555 Triglyceride 0.992 0 0.982 0.0099 Water 29.762 0 29.464 0.297

Solids exiting the desolventizer are fed to a dryer. The vapor exiting the desolventizer contains 0.55 tons/hr of hexane and 1.102 tons/hr of water. This stream is condensed and fed to a decanter. The water-rich phase exiting the decanter contains about 360 ppm of hexane. This stream is fed to a distillation column where the hexane is removed from the water-rich stream. The hexane enriched stream exiting the top of the distillation column is condensed and fed to the decanter. The organic-rich stream exiting the decanter is fed to a distillation column. Steam (11.02 tons/hr) is fed to the bottom of the distillation column. The composition of the overhead and bottom products for this column are shown in Table 75. Table values are tons/hr.

TABLE 75 Bottoms Overheads Fatty acids 0.0981 0 Fatty acid butyl esters 2.8232 0 Hexane 0.0011 11.12 Triglyceride 0.9812 0 Water 0 11.02

Example 63 Solids Extraction

Preparation of Hydrous Isobutanol

Into a 100 mL volumetric flask, 65 g of anhydrous reagent grade isobutanol (sourced from Aldrich) was combined with 10 g of distilled water and shaken until a clear colorless homogeneous phase resulted. Another 10 g of distilled water was added to the volumetric flask and shaken again resulting in two persistent clear colorless liquid layers. The top layer is considered to be hydrous isobutanol containing typically 20 wt % moisture and the bottom layer is predominantly water with typically 8 wt % dissolved alcohol.

Extraction Using Screen Filtration and Displacement Wash

A fermentation was completed using recycled fatty acid (Example 19). A 185 g portion representative of the resulting heterogeneous mixture was removed and passed through a 80 MESH screen dish supported and sealed within a Nalgene® plastic filter funnel over 5 minutes using slight vacuum (−20 in H₂O) on the underside. The filtrate partitioned into 90.5 g of a reddish brown oil phase and 50.9 g of a hazy aqueous phase containing dispersed fines but no settling particulates. A wet cake remained on the screen dish. A sample of 1.5 g of this unwashed wet cake was removed and air dried. Hydrous isobutanol (23 g) was drawn from the top layer inside the volumetric flask and passed through the wet cake over 5 minutes while mild vacuum on the underside of the screen dish was maintained until no more liquid droplets were collected. The total filtrate mass of 18 g consisted of a small amount of an immiscible bottom hazy aqueous layer and a yellow clear hydrous isobutanol layer. The wet cake was removed from the screen dish and a total mass of 38.4 g was recovered. A sample of 1.5 g of this washed wet cake was removed and air dried. The dried sample of unwashed solids was analyzed and found to contain 53.35 wt % total fat on a triglyceride basis and the dried sample of washed solids was analyzed and found to contain 15.9 wt % total fat on a triglyceride basis.

Extraction Using Centrifugation and Reslurry Wash

A fermentation was completed using recycled fatty acid (Example 19). A 225 g portion representative of the resulting heterogeneous mixture was removed and centrifuged using a Beckman Coulter Allegra 64R machine at 10,000 rpm for 10 minutes. A clear reddish brown oil phase amounting to 67.2 g was decanted off. The remaining material was centrifuged again and 95.1 g of a cloudy aqueous centrate was decanted off. A 1.5 g sample of the wet solids was removed and air dried and 56.5 g were recovered and transferred to a 400 mL beaker. Hydrous isobutanol (20 g) drawn from the top layer inside the volumetric flask was added to the beaker to repulp the wet solids and stirring was carried out for 5 minutes. Another 32 g of hydrous isobutanol along with 32 g of the centrate were added and the solids were agitated in aqueous suspension beneath a quiescent organic layer for 5 minutes. The mixture was then centrifuged at 10,000 rpm for 10 minutes to decant off a clear yellow hydrous isobutanol layer and centrifuged again in order to isolate and dry a 1.5 g sample of washed wet solids. The dried sample of unwashed wet solids were analyzed and found to contain 21.6 wt % total fat on a triglyceride basis and the dried sample of washed wet solids were analyzed and found to contain 4.04 wt % total fat on a triglyceride basis.

Example 64 Removal of Corn Oil by Removing Undissolved Solids

Approximately 1000 g of liquefied corn mash was prepared in a 1 L glass, jacketed resin kettle. The kettle was set up with mechanical agitation, temperature control, and pH control. The following protocol was used: mixed ground corn with tap water (26 wt % corn on a dry basis), heated the slurry to 55° C. while agitating, adjusted pH to 5.8 with either NaOH or H₂SO₄, added alpha-amylase (0.02 wt % on a dry corn basis), continued heating to 85° C., adjusted pH to 5.8, held at 85° C. for 2 hrs while maintaining pH at 5.8, cool to 25° C. The corn used was whole kernel yellow corn from Pioneer (3335). It was ground in a hammer-mill using a 1 mm screen. The moisture content of the ground corn was measured to be about 11.7 wt %, and the starch content of the ground corn was measured to be about 71.4 wt % on a dry corn basis. The alpha-amylase enzyme was Liquozyme® SC DS from Novozymes (Franklinton, N.C.). The total amounts of the ingredients used were: 294.5 g of ground corn (11.7% moisture), 705.5 g of tap water, and 0.059 g of Liquozyme® SC DS. H₂O (4.3 g) was added to dilute the enzyme, and a total of 2.3 g of 20% NaOH solution was added to control pH. About 952 g of mash was recovered. Note that there were losses due to mash sticking on walls of kettle and CF bottles.

The liquefied corn mash was centrifuged at 5000 rpm (7260 g's) for 30 minutes at 40° C. to remove the undissolved solids from the aqueous solution of oligosaccharides. Removing the solids by centrifugation also resulted in the removal of free corn oil as a separate organic liquid layer on top of the aqueous phase. Approximately 1.5 g of corn oil was recovered from the organic layer floating on top of the aqueous phase. It was determined by hexane extraction that the ground corn used to produce the liquefied mash contained about 3.5 wt % corn oil on a dry corn basis. This corresponds to about 9 g of corn oil fed to the liquefaction process with the ground corn.

Approximately 1 g of corn oil was recovered from the organic layer floating on top of the aqueous phase. About 617 g of liquefied starch solution was recovered leaving about 334 g of wet cake. The wet cake contained most of the undissolved solids that were in the liquefied mash. The liquefied starch solution contained about 0.2 wt % undissolved solids. The wet cake contained about 21 wt % undissolved solids. The wet cake was washed with 1000 g of tap water to remove the oligosaccharides still in the cake. This was done by mixing the cake with the water to form a slurry. The slurry was then centrifuged under the same conditions used to centrifuge the original mash in order to recover the washed solids. Removing the washed solids by centrifugation also resulted in the removal of some additional free corn oil as a separate organic liquid layer on top of the aqueous phase. Corn oil was recovered from the organic layer floating on top of the aqueous phase.

The wet solids were washed two more times using a 1000 g of tap water each time to remove essentially all of the liquefied starch. The final washed solids were dried in a vacuum oven overnight at 80° C. and about 20 inches Hg vacuum. The amount of corn oil remaining in the dry solids, presumably still in the germ, was determined by hexane extraction. It was measured that a 3.60 g sample of relatively dry solids (about 2 wt % moisture) contained 0.22 g of corn oil. This result corresponds to 0.0624 g corn oil/g dry solids. This was for washed solids which means there are no residual oligosaccharides in the wet solids. After centrifuging the liquefied corn mash to separate the layer of free corn oil and the aqueous solution of oligosaccharides from the wet cake, it was determined that about 334 g of wet cake containing about 21 wt % undissolved solids remained. This corresponds to the wet cake comprising about 70.1 g of undissolved solids. At 0.0624 g corn oil/g dry solids, the solids in the wet cake should contain about 4.4 g of corn oil.

In a separate experiment, a 26 wt % dry corn mash stream was generated using enzyme loads consistent with the liquefaction described above. This liquefied mash stream was processed through a Flottwegg centrifuge where the liquefied mash was separated into an oil stream, a thin mash stream, and a wet cake stream. The rate of oil recovery was roughly 1.1 lbm/bushel of corn to 1.5 lbm/bushel of corn. This recovery percentage is roughly 50% to 67% of the total oil entering the process. This recovery from the front end of the process is a higher percentage than typically recovered from the back end of the process (e.g., typical values of 0.4 lbm/bushel of corn representing 20% of the oil entering the process). Corn oil removed by this process has not gone through fermentation nor distillation and as such represents a cleaner corn oil stream.

Example 65 Lipid Analysis

Lipid analysis was conducted by conversion of the various fatty acid-containing compound classes to fatty acid methyl esters (“FAMEs”) by transesterification. Glycerides and phospholipids were transesterified using sodium methoxide in methanol. Glycerides, phospholipids, and free fatty acids were transesterified using acetyl chloride in methanol. The resulting FAMEs were analyzed by gas chromatography using an Agilent 7890 GC fitted with a 30-m×0.25 mm (i.d.) OMEGAWAX™ (Supelco, SigmaAldrich, St. Louis, Mo.) column after dilution in toluene/hexane (2:3). The oven temperature was increased from 160° C. to 200° C. at 5° C./min then 200° C. to 250° C. (hold for 10 min) at 10° C./min. FAME peaks recorded via GC analysis were identified by their retention times, when compared to that of known methyl esters (MEs), and quantitated by comparing the FAME peak areas with that of the internal standard (C15:0 triglyceride, taken through the transesterification procedure with the sample) of known amount. Thus, the approximate amount (mg) of any fatty acid FAME (“mg FAME”) is calculated according to the formula: (area of the FAME peak for the specified fatty acid/area of the 15:0 FAME peak)*(mg of the internal standard C15:0 FAME). The FAME result can then be corrected to mg of the corresponding fatty acid by dividing by the appropriate molecular weight conversion factor of 1.052. All internal and reference standards are obtained from Nu-Chek Prep, Inc.

The fatty acid results obtained for samples transesterified using sodium methoxide in methanol are converted to the corresponding triglyceride levels by multiplying the molecular weight conversion factor of 1.045. Triglycerides generally account for approximately 80 to 90% of the glycerides in the samples studies for this example, with the remainder being diglycerides. Monoglyceride and phospholipid contents are generally negligible. The total fatty acid results obtained for a sample transesterified using acetyl chloride in methanol are corrected for glyceride content by subtracting the fatty acids determined for the same sample using the sodium methoxide procedure. The result is the free fatty acid content of the sample.

The distribution of the glyceride content (monoglycerides, diglycerides, triglycerides, and phospholipids) is determined using thin layer chromatography. A solution of the oil dissolved in 6:1 chloroform/methanol is spotted near the bottom of a glass plate precoated with silica gel. The spot is then chromatographed up the plate using a 70:30:1 hexane/diethyl ether/acetic acid solvent system. Separated spots corresponding to monoglycerides, diglycerides, triglycerides, and phospholipids are then detected by staining the plate with iodine vapor. The spots are then scraped off the plate, transesterified using the acetyl chloride in methanol procedure, and analyzed by gas chromatography. The ratios of the totaled peak areas for each spot to the totaled peak areas for all the spots are the distribution of the various glycerides.

Example 66

This example illustrates the recovery of by-products from mash. Corn oil was separated from mash under the conditions described in Example 64 with the exception that a tricanter centrifuge (Flottweg Z23-4, bowl diameter 230 mm, length to diameter ratio 4:1) was used with these conditions:

Bowl Speed: 5000 rpm Differential Speed: 10 rpm Feed Rate: 3 gpm Phase Separator Disk: 138 mm Impeller Setting 144 mm.

The corn oil separate had 81% triglycerides, 6% free fatty acids, 4% diglyceride, and 5% total of phospholipids and monoglycerides as determined by the methods described in Example 65 and thin layer chromatography.

The solids separated from mash under the conditions described above had a moisture content of 58% as determined by weight loss upon drying and had 1.2% triglycerides and 0.27% free fatty acids as determined by the method described in Example 65.

The composition of solids separated from whole stillage, oil extracted between evaporator stages, by-product extractant and Condensed Distillers Solubles (CDS) in Table 78 were calculated assuming the composition of whole stillage shown in Table 76 and the assumptions in Table 77 (separation at tricanter centrifuge. The values of Table 75 were obtained from an Aspen Plus® model (Aspen Technology, Inc., Burlington, Mass.). This model assumes that corn oil is not extracted from mash. It is estimated that the protein content on a dry basis of cells, dissolved solids, and suspended solids is approximately 50%, 22%, and 35.5%, respectively. The composition of by-product extractant is estimated to be 70.7% fatty acid and 29.3% fatty acid isobutyl ester on a dry basis.

TABLE 76 Component Mass % Water 57.386% Cells 0.502% Fatty acids 6.737% Isobutyl esters of fatty acids 30.817% Triglyceride 0.035% Suspended solids 0.416% Dissolved solids 4.107%

TABLE 77 Hydrolyzer Thin feed stillage Solids Organics 99.175%    0.75% 0.08% Water and dissolved solids 1%  96%   3% Suspended solids and cells 1%   2%  97%

TABLE 78 Stream C. protein triglyceride FFA FABE Whole stillage wet cake 40% trace  0.5%  2.2% Oil at evaporator  0% 0.08% 16.1% 73.8% CDS 22% trace % 0.37% 1.71%

Example 67

This example illustrates the recovery of product alcohol from the butyl ester of fatty acid using base hydrolysis. Corn oil fatty acid/butyl ester of fatty acid extracting solvent is isolated from the fermentation broth after fermentation is complete. A dilute sodium hydroxide solution is added to the COFA/FABE mixture. The moles of sodium hydroxide used are roughly 10% in excess of the moles of fatty acid and FABE combined. The reaction mass is maintained at 90° C. for several hours until all of the FABE has reacted with water to make isobutanol and the sodium salt of corn oil fatty acid. After 2 hours, a dilute sulfuric acid solution is added. The moles of sulfuric acid is equal to the moles of sodium hydroxide added in the previous step. The reaction is again held for several hours. The resulting solution is then available for further purification.

Example 68 Production of Diol Esters by Lipase-Catalyzed Reaction of Diol and Oleic Acid

Reaction mixtures containing aqueous 2-(N-morpholino)ethanesulfonic acid buffer (MES, 0.20 M, pH 5.5), lipase (0 ppm or 10 ppm Lipolase® 100 L; Thermomyces (Humicola) lanuginosus lipase from Novozymes), oleic acid (99% or 90% purity (pur.), Alfa Aesar), and a diol selected from the group of 1,2-ethanediol (EDO), 1,3-propanediol (PDO), and 1,4-butanediol (BDO) (Table 79) were stirred at 30° C., and samples were withdrawn from each reaction mixture at 0 h, 21 h and 72 h, immediately centrifuged, and the aqueous and organic layers separated and analyzed for diol and the corresponding mono- and di-oleate esters of diol. Aqueous phase samples were analyzed by HPLC, where measured substrate amounts are reported as a percentage of the initial amount present in the 0 h aqueous phase sample as determined from integrated peak areas in peak area units (PAU) (Table 80).

TABLE 79 Diol and oleic acid esterification reaction mixtures lipase aq. MES diol Oleic Acid Oleic Acid Flask (ppm) (g) diol (g) (g) (% purity) A 10 46.1 PDO 3.6 14.47 99 B 10 46.1 BDO 3.6 14.47 99 C 10 46.1 EDO 3.6 14.47 99 E 0 46.1 PDO 3.6 14.47 99 F 0 46.1 BDO 3.6 14.47 99 G 0 46.1 EDO 3.6 14.47 99

TABLE 80 Diol concentrations in aqueous phase as percent of initial concentration. lipase (ppm) time (h) EDO (% PAU) PDO (% PAU) BDO (% PAU) 10 0 100 100 100 10 21 99 94 86 10 72 97 85 67 0 0 100 100 100 0 21 100 101 100 0 72 100 101 100

Oleic acid-phase samples were mixed at 1:9 (wt:wt) with isopropanol containing methyl pentadecanoate (C15:0 FAME) as internal standard and analyzed by GC/MS to generate TIC (“total ion count”) chromatograms of the 72 h samples containing only internal standard (A), and internal standard with EDO (B), PDO (C) and BDO (D); in comparison to the sample containing only internal standard (C15:0 FAME, A), all chromatograms exhibited a significant peak eluting at RT (retention time)˜18.6 min, corresponding to oleic acid. The chromatogram of EDO (B) showed two significant peaks at RT˜22.9 min and RT˜49.6 min, of PDO (C) at RT˜25.6 min and RT˜53.2 min, and of BDO (D) at RT˜29.1 min and RT˜59.8 min, corresponding to the mono- and dioleyl diol esters, respectively. Expected elemental formula and associated masses of the mono- and dioleyl diol esters of the respective compounds are reported in Table 81.

TABLE 81 Elemental formulas for the mono- and dioleyl diol esters of respective molecules and exact masses as determined by an exact mass calculator. elemental Mr Mr Mr diol formula [ ] [g/mol] mono* [g/mol] di* [g/mol] EDO C₂H₆O₂ 62.04 C₂₀H₃₈O₃ 326.28 C₃₈H₇₀O₄ 590.53 PDO C₃H₈O₂ 76.05 C₂₁H₄₀O₃ 340.30 C₃₉H₇₂O₄ 604.54 BDO C₄H₁₀O₂ 90.07 C₂₂H₄₂O₃ 354.31 C₄₀H₇₄O₄ 618.56 Mono* = monooleyl ester, di* = dioleyl ester

Mass spectra were determined for the peaks at RT=22.9, 25.6 and 29.1 min of the EDO, PDO and BDO chromatograms, respectively. Significant mass peaks were found at 326 (A), 340 (B) and 354 (C) amu. These masses correlate with the calculated molecular ion of the corresponding monooleyl esters (Table 3), indicating that these mass peaks correspond to the monooleyl esters of the respective compounds. The measured mass spectrum of the peak at RT=25.6 min in the PDO chromatogram was compared to the NIST 2008 standard mass spectrum of oleic acid 3-hydroxypropyl ester and the correspondence of peaks confirmed the identity of the peak as the monooleyl ester of PDO.

High mass spectra were determined for peaks eluting at RT=49.6, 53.2 and 59.8 min in the EDO, PDO and BDO chromatograms, respectively. Significant signals were obtained at 590, 604 and 618 amu, respectively, representing masses that correspond to the molecular ion of the dioleyl esters of the respective molecules. Peaks were quantified by integrating the GC/MS total ion count (TIC) signal. Results are shown in Table 82.

TABLE 82 Peak areas from the integrated total ion count signal of the identified mono- and dioleyl esters. time monooleyl ester dioleyl ester diol [h] [TIC] [TIC] EDO 0 h n.d. n.d. EDO 22 h  9856195 127935891 EDO 72 h 23047769 310072763 PDO 0 h n.d. n.d. PDO 22 h 23232621 395169664 PDO 72 h 72227588 969655491 BDO 0 h n.d. n.d. BDO 22 h 107428388 591046462 BDO 72 h 153608396 1765024310  n.d. = not detected

Example 69 Quantitative Analysis of Diol Esters Produced by Lipase-Catalyzed Reaction of Diol and Oleic Acid Calculation of Concentrations of Monooleyl (MOE) and Dioleyl Esters (DIE) in the Oleic Acid Phase of a Lipase-Catalyzed Reaction of Diol and Oleic Acid

The biochemical reaction system of Example 69 can be described by two reactions:

DIOL_(aq)+OA_(org)

H₂O_(org)+MOE_(org)  R1

MOE_(org)+OA_(org)

H₂O_(org)+DIE_(org)  R2

With very high concentrations of oleic acid (OA_(org)˜3.2 M) and constant concentration of H₂O in the oleic acid (at equilibrium concentration with the aqueous phase), the reaction system can be further simplified according to:

DIOL_(aq)

MOE_(org)  R1

MOE_(org)

DIE_(org)  R2

Both reactions are reversible, with either DIOL_(aq), MOE_(org) or DIE_(org) competing to bind to the enzyme. This mechanism can be described by a reversible Michaelis-Menten kinetics (Haldane relationship),

$\frac{P}{t} = \frac{{v_{\max,{forward}} \cdot \frac{S}{K_{m,S}}} - {v_{\max,{reverse}} \cdot \frac{P}{K_{m,P}}}}{1 + \frac{S}{K_{m,S}} + \frac{P}{K_{m,P}}}$

with P=MOE_(org) and S=DIOL_(aq) in R1, and P=DIE_(org) and S=MOE_(org) in R2. At equilibrium, the educt and product concentrations in R1 and R2 do not change with time, respectively, and the following relationship holds:

$K_{eq} = {\frac{P_{eq}}{S_{eq}} = \frac{v_{\max,{forward}} \cdot K_{m,P}}{v_{\max,{reverse}} \cdot K_{m,S}}}$

Plotting the product concentration of a reversible Michaelis-Menten kinetics (Haldane relationship) over time with an initial product concentration of zero yields a hyperbolic curve with the equilibrium concentration as the end point. This calculation applies to both of the reaction sequences R1 and R2. Consequently a similar hyperbolic curve can be expected if instead of the final product concentrations the net catalyzed number of reactions of the lipase in R1 and R2 is considered. Based on the calculated concentrations of mono- and dioleyl esters of EDO, PDO and BDO (Table 84), a plot of the net reaction numbers (given in a molar concentration) for sampling time t=0 h, 21 h or 72 h demonstrate that the reaction number in all three reaction systems increases over time, and deviations between a hyperbolic fit of this data and linear, zero-order kinetic fit of this same data indicates that the reaction systems at t=72 h are not at equilibrium. The concentration of lipase added to the reaction systems was used to determine observed average specific enzyme activity (from the approximated zero order kinetics) of 1,902, 5,928 and 10,962 U/g, respectively, with EDO, PDO and BDO as substrate, under the applied reaction conditions.

Relative percents of the diol in aqueous phase samples reported in Table 2 (Example 1) were converted to absolute diol concentrations. Where 3.6 g of EDO, PDO, and BDO were each mixed with 46.1 mL of aqueous buffer solution, and where the resulting aqueous diol mixture had a density of ca. 1.0 g/cm³ and neither water nor diols were extracted in any significant quantity into the oleic acid phase. Calculated diol concentrations in the aqueous phase for EDO, PDO and BDO are listed in Table 83 below.

TABLE 83 Concentrations of EDO, PDO and BDO in the experiment calculated from measured HPLC peaks areas in [PAU] derived from the initially added amount of the respective diol. c(EDO) c(PDO) c(BDO) time [mM] [mM] [mM] w lipase t = 0 h 1168 952 804 t = 21 h 1151 900 694 t = 72 h 1130 809 541 w/o lipase t = 0 h 1168 952 804 t = 21 h 1166 963 806 t = 72 h 1167 958 807

To determine the amount of monooleyl and dioleyl esters formed, all measurements of the EDO, PDO and BDO samples were used to determine a single response factor (RF) for monooleyl as well as for the dioleyl esters, RF1 and RF2, respectively. The two RFs correlate total ion counts of the monooleyl and dioleyl esters determined in [PAU] in GC/MS analysis (Example 68, Table 82) with their respective concentrations.

Total amount of formed esters was determined from the molar amount of diol consumed (DC). For every sample point i acquired at sampling time t=0 h, 21 h or 72 h with either EDO, PDO or BDO, the molar balance was calculated as follows:

RF1×[TIC area of monooleyl ester]_(i)+RF2×[TIC area of dioleyl ester]_(i)=DC_(i)

The samples at t=21 h and 72 h for EDO, PDO and BDO provide six data points for determining RF1 and RF2. The resulting over-determined linear equation system with 6 equations and 2 unknowns was solved with the “linsolve”-algorithm in MATLAB (Version 7.10.0.499). The obtained values were, respectively: RF1=1.24E-06 mM/[PAU], and RF2=3.51 E-07 mM/[PAU]. These response factors describe the concentrations of mono and dioleyl esters in the organic phase and incorporate a 1:9 (wt/wt) dilution of the organic phase with isopropyl alcohol containing methyl pentadecanoate internal standard for GC/MS analysis. Response factors for undiluted samples and assuming a constant density of 1.000 g/ml of the solutions results in RF1=1.24E-07 mM/[PAU], and RF2=3.51E-08 mM/[PAU]. Internal standard measurements were not applied to correct these values.

The response factors were used to calculate the concentration of mono (c(MOE)_(calc)) and dioleyl esters (c(DIE)_(calc)) in the organic phase, as well as the number of lipase catalyzed reaction events c(reaction) given in [mM] (Table 84). The corresponding predicted consumption of EDO, PDO and BDO in the aqueous phase c(total)_(calc) was subsequently calculated and compared to the measured values c(diol)_(meas). Predicted and measured values were found to be in good agreement (Table 84). Most significant deviations were found for EDO. As BDO had the highest values and consequently the most weight in the calculation, the determined RF1 and RF2 may discriminate mostly against the smaller EDO values.

TABLE 84 Molecules, samples and calculated concentrations of monooleyl (MOE) and dioleyl esters (DIE), as well as reaction events represented in [mM] in the organic oleic acid phase. Expected consumption of respective diol in the aqueous phase c(total)_(calc) is compared with the measured diol consumption c(diol)_(meas). organic phase aqueous phase c(reac- C(to- mole- C(MOE)_(calc) C(DIE)_(calc) tion) tal)_(calc) C(diol)_(meas) cule sample [mM] [mM] [mM] [mM] [mM] EDO t = 0.0 0.0 0.0 0.0 0.0 0 h t = 12.2 44.9 102.0 18.6 16.6 21 h t = 28.5 108.9 246.2 44.7 38.0 72 h PDO t = 0.0 0.0 0.0 0 h t = 28.7 138.7 306.2 54.5 52.5 21 h t = 89.3 340.4 770.1 139.8 143.0 72 h BDO t = 0.0 0.0 0.0 0.0 0.0 0 h t = 132.9 207.5 547.8 110.7 110.5 21 h t = 190.0 619.6 1429.2 263.4 263.5 72 h

Example 70 Reactive Liquid Extraction of 1,3-Propanediol Produced During Biocatalyst Growth on Glucose

A PDO-producing strain of E. coli called TTab/pSYCO109 was described in the published US patent application US 20110256598, which is incorporated herein by reference. This strain is E. coli strain TTab carrying plasmid pSYCO109. Construction of the TTab strain, described in US 2011/0256598, was by deletion of the aldB gene from strain TT aldA, which is a strain with aldA deletion, whose construction is described in U.S. Pat. No. 7,371,558 (Example 17), which is incorporated herein by reference. An aldB deletion was made in E. coli strain MG1655 by replacing 1.5 kb of the coding region with the FRT-CmR-FRT cassette of the pKD3 plasmid (Datsenko and Wanner, Proc. Natl. Acad. Sci. USA 97:6640-6645, 2000). Recombinant strains were selected on LB plates with 12.5 mg/L of chloramphenicol and the deletion confirmed by PCR analysis. A P1 lysate was prepared and used to move the mutation to the TT aldA strain to form the TT aldAAaldB::Cm strain. A chloramphenicol-resistant clone was checked by genomic PCR to verify the incorporation of the aldB deletion. The chloramphenicol resistance marker was removed using the FLP recombinase (Datsenko and Wanner, supra) to create the TTab strain. As described in the cited references, strain TTab is a derivative of E. coli strain FM5 (ATCC® No. 53911) and contains the following modifications:

deletion of glpK, gldA, ptsHl, crr, edd, arcA, mgsA, qor, ackA, pta, aldA and aldB genes;

upregulation of galP, glk, btuR, ppc, and yqhD genes; and

downregulation of gapA gene.

Strain TTab was transformed with pSYCO109 (SEQ ID NO:203), which is described in U.S. Pat. No. 7,371,558. The essential elements are derived from the dha regulon (including coding regions for a dehydratase activity, a reactivation activity, and a 1,3-propanediol oxidoreductase) isolated from Klebsiella pneumoniae and from Saccharomyces cerevisiae. It contains the open reading frames dhaB1 (the large or “a” subunit of glycerol dehydratase), dhaB2 (the medium or “β” subunit of glycerol dehydratase), dhaB3 (the small or “γ” subunit of glycerol dehydratase), dhaX, orfX, DAR1 (glycerol-3-phosphate dehydrogenase), and GPP2 (glycerol-3-phosphatase) arranged in three separate operons.

Pre-culture of E. coli TTab/pSyco109 was started by inoculating 1 frozen seed vial (approx. 1 mL of a glycerol stock) into 10 ml of LB medium with 50 μg/ml spectinomycin in a 125 ml shake flask. The culture was incubated at 36° C. in an innova 4230 shaker (New Brunswick Scientific, Edison, N.J.) at 260 rpm for 13.5 h. OD was determined at λ=600 nm in an Ultraspec 3000 spectrophotomer from Pharmacia Biotech (Piscataway, N.J.). Composition of the SF medium was 42 mM Na₂HPO₄, 24 mM KH₂PO₄, 9 mM NaCl, 19 mM NH₄Cl, 1 mM MgSO₄, 0.1 mM CaCl₂, 0.5 mg/L thiamine, 0.1 mg/L vitamin B12, 50 mg/L spectinomycin and 10 g/L glucose. Multiple shake flasks (250 mL) were filled with 22 mL of SF medium, then the flasks were inoculated with 61 μL of the E. coli TTab/pSyco109 pre-culture to give a starting OD of approximately 0.010. Shake flasks were incubated in an innova 4230 shaker (New Brunswick Scientific, Edison, N.J.) at 34° C. with a rotating speed of 260 rpm. The growth profile as sampled from multiple shake flasks at different time points is depicted in Table 85.

TABLE 85 Growth profile of E. coli TTab/pSyco109, as sampled from multiple shake flask cultures at different time points. EPT = elapsed process time. EPT [h] OD600 0.00 0.009 9.58 0.022 13.50 0.038 17.25 0.074 20.08 0.144 20.75 0.179

At an elapsed process time (EPT) of 20.75 h, 5 mL of oleic acid was added to one of the shake flask cultures (SF control), and 5 mL oleic acid and 250 μL of a solution of 2.0 mg/mL of Thermomyces lanuginosus lipase (Lipolase™ 100L, Novozymes, Bagsvaerd, DK) in 10 mM potassium phosphate buffer (pH 7.0) (25 ppm) was added to another shake flask culture (SF enzyme). Due to interference by the second phase formed by oleic acid, no further OD measurements were made. Oleic acid served both as the carboxylic acid for esterification, and as an organic phase extractant. The substrate glucose and the major products glycerol and PDO in the aqueous broth were analyzed by HPLC (Table 86). It was observed that glucose was completely consumed in both fermentations and glycerol and PDO concentrations measured in the aqueous broth were higher for the control fermentation (SF control) than for the fermentation with lipase added (SF enzyme).

TABLE 86 Concentrations of glucose, glycerol and PDO in the aqueous phase as determined by HPLC. EPT = elapsed process time. EPT Glucose Glycerol PDO [h] [mM] [mM] [mM] SF control sample 1 0.00 58.36 0.60 0.00 sample 2 20.08 58.33 0.56 0.00 sample 3 (with extractant) 20.75 58.43 3.48 0.00 sample 4 (with extractant) 33.33 52.26 13.06 2.78 sample 5 (with extractant) 104.83 0.00 82.17 24.38 sample 6 (with extractant) 128.83 0.00 94.76 28.27 SF enzyme sample 1 0.00 58.36 0.60 0.00 sample 2 20.08 58.30 0.58 0.00 sample 3 (with extractant) 20.75 58.34 3.32 0.00 sample 4 (with extractant) 33.33 54.34 9.72 1.70 sample 5 (with extractant) 104.83 0.00 64.58 18.48 sample 6 (with extractant) 128.83 0.00 73.00 19.35

Analysis of the final extractant phase from the SF control and SF enzyme fermentations (samples 6) by GC/MS indicated that a significant amount of 1,3-PDO dioleyl ester was formed and extracted in the SF enzyme experiment as compared to the SF control experiment (Table 87).

TABLE 87 Total ion counts (TIC) of 1,3-PDO monooleyl ester and 1,3-PDO dioleyl ester in the extractant of samples 6. 1,3 PDO 1,3 PDO EPT monooleyl ester dioleyl ester [h] [TIC] [TIC] SF control: sample 6 128.83 n.d. n.d. SF enzyme: sample 6 128.83 n.d. 511,412,000 n.d. = not detected

A response factor of 1.24E-07 mM/TIC for the 1,3-PDO monooleyl ester and 3.51 E-08 mM/TIC for the 1,3-PDO dioleyl ester in oleic acid, respectively, was employed to calculate concentrations in the final extractant phase for each fermentation (Table 88).

Table 88. Concentrations of 1,3-PDO monooleyl ester and 1,3-PDO dioleyl ester in the extractant phase of sample 6 as determined with response factors of 1.24E-07 mM/TIC and 3.51 E-08 mM/TIC, respectively.

1,3 PDO 1,3 PDO EPT monooleyl ester dioleyl ester [h] [mM] [mM] SF control: sample 6 128.83 0.0 0.0 SF enzyme: sample 6 128.83 0.0 18.0

Example 71 Reactive Liquid Extraction of 1,3-Propanediol Produced Subsequent to Biocatalyst Growth on Glucose

Multiple shake flasks (250 mL) containing SF medium were prepared and inoculated with E. coli TTab/pSyco109 pre-culture following the same procedure as described in Example 70. Shake flasks were incubated for elapsed process time (EPT) of 34.75 h (Table 89) in an innova 4230 shaker (New Brunswick Scientific, Edison, N.J.) at 34° C. with a rotating speed of 260 rpm and the growth monitored by OD600.

TABLE 89 Growth profile of E. coli TTab/pSyco109, as sampled from multiple shake flask cultures at different time points. EPT = elapsed process time. EPT [h] OD600 0.00 0.009 9.58 0.022 13.50 0.038 17.25 0.074 20.08 0.144 20.75 0.179 33.33 3.188 34.75 3.328

After complete consumption of glucose at an EPT of 34.75 h, 9.5 mL of oleic acid was added to one of the shake flask cultures (SF control), 9.5 mL oleic acid and 250 μL of a solution of 2.0 mg/mL of Thermomyces lanuginosus lipase (Lipolase™ 100L, Novozymes, Bagsvaerd, DK) in 10 mM potassium phosphate buffer (pH 7.0) (25 ppm final concentration) was added to another of the shake flask cultures (SF enzyme 1), and 9.5 mL oleic acid and 250 μL of a solution of 2.0 mg/mL of Aspergillus tubingensis LIP3 lipase (Genencor, Palo Alto) in 50 mM sodium acetate (pH 5.0, with 0.1% BSA and 1.2% NaCl) (25 ppm final concentration) was added to yet another shake flask culture (SF enzyme 2). Due to interference by the second phase formed by oleic acid, no further OD measurements were made. The substrate glucose and the major products glycerol, PDO and formate were analyzed in the aqueous broth by HPLC (Table 90). In all three experiments glucose concentration during addition of oleic acid was zero. However, PDO concentrations measured in the aqueous broth were found significantly higher in the control experiment (SF control) than for the two experiments with added lipase enzyme (SF enzyme 1 and SF enzyme 2).

TABLE 90 Concentrations of glucose, glycerol, PDO and formate in aqueous phase as determined by HPLC. EPT = elapsed process time. EPT Glucose Glycerol PDO Formate [h] [mM] [mM] [mM] [mM] SF control sample 1 0.00 58.36 0.60 0.00 0.00 sample 2 20.08 58.31 0.57 0.00 0.00 sample 3 34.75 0.00 41.18 31.30 0.00 sample 4 (with 108.75 0.00 51.88 38.74 0.00 extractant) sample 5 (with 130.75 0.00 55.85 42.24 1.38 extractant) SF enzyme 1 sample 1 0.00 58.36 0.60 0.00 0.00 sample 2 20.08 58.31 0.57 0.00 0.00 sample 3 34.75 0.00 41.21 31.98 0.00 sample 4 (with 108.75 0.00 52.16 35.01 1.14 extractant) sample 5 (with 130.75 0.00 56.87 37.50 1.53 extractant) SF enzyme 2 sample 1 0.00 58.36 0.60 0.00 0.00 sample 2 20.08 58.31 0.57 0.00 0.00 sample 3 34.75 0.00 41.55 30.53 0.00 sample 4 (with 108.75 0.00 49.57 33.84 0.00 extractant) sample 5 (with 130.75 0.00 52.95 35.05 0.00 extractant)

Analysis of the final extractant phase from the SF control, SF enzyme 1 and SF enzyme 2 fermentations (samples 5) by GC/MS detected no 1,3-PDO monooleyl ester or 1,3-PDO dioleyl ester in the no enzyme controls. There was also no mono-ester in the enzyme samples, but significant amounts of the dioleyl ester, indicating esterification at both hydroxyl positions (Table 91).

TABLE 91 Total ion counts of 1,3-PDO monooleyl ester and 1,3- PDO dioleyl ester in the extractant of samples 5. 1,3 PDO 1,3 PDO EPT monooleyl ester dioleyl ester [h] [TIC] [TIC] SF control: sample 5 130.75 n.d. n.d. SF enzyme 1: sample 5 130.75 n.d. 203,187,430 SF enzyme 2: sample 5 130.75 n.d. 152,520,090 n.d. = not detected

A response factor of 1.24E-07 mM/TIC for 1,3-PDO monooleyl ester and 3.51 E-08 mM/TIC for 1,3-PDO dioleyl ester in oleic acid, respectively, was employed to calculate concentrations in the final extractant phase for each fermentation (Table 92).

TABLE 92 Concentrations of 1,3-PDO monooleyl ester and 1,3-PDO dioleyl ester in the extractant of samples 5 as determined with response factors of 1.24E−07 mM/TIC and 3.51E−08 mM/TIC, respectively. 1,3-PDO 1,3-PDO EPT monooleyl ester dioleyl ester [h] [mM] [mM] SF control: sample 5 130.75 0.0 0.0 SF enzyme 1: sample 5 130.75 0.0 7.1 SF enzyme 2: sample 5 130.75 0.0 5.4 

What is claimed is:
 1. A method for recovering a diol from a fermentation process comprising: a) providing a fermentation medium or fermentation product broth containing a diol; b) contacting the diol in the fermentation medium or fermentation product broth with at least one carboxylic acid and at least one catalyst capable of esterifying the carboxylic acid with the diol to form diol esters of the carboxylic acid in the presence of an organic solvent which is present at a concentration sufficient to produce a two-phase mixture; c) separating the diol ester-containing organic phase from the aqueous phase; and d) hydrolyzing the diol ester into carboxylic acid and diol; and e) recovering the diol.
 2. A method for producing a diol from a biomass feedstock comprising: a) providing a biomass feedstock; b) liquefying the biomass feedstock to create a feedstock slurry comprising oligosaccharides; c) saccharifying the oligosaccharides of the feedstock slurry to produce fermentable sugars; d) fermenting the fermentable sugars using a microorganism to produce a diol in a fermentation medium or a fermentation product broth; e) contacting the diol in the fermentation medium or fermentation product broth with at least one carboxylic acid and at least one catalyst capable of esterifying the carboxylic acid with the diol to form diol esters of the carboxylic acid in the presence of an organic solvent which is present at a concentration sufficient to produce a two-phase mixture; f) separating the diol ester-containing organic phase from the aqueous phase; g) hydrolyzing the diol ester into carboxylic acid and diol; and h) recovering the diol. wherein optionally steps (c) and (d) occur concurrently, optionally steps (d) and (e) occur concurrently, or optionally steps (c), (d), and (e) occur concurrently.
 3. The method of claim 1 or 2 wherein the organic solvent comprises said carboxylic acid and at least one non-reactive organic solvent.
 4. The method of claim 3 wherein the non-reactive organic solvent is other than carboxylic acid or alcohol.
 5. The method of claim 1 or 2 wherein the organic solvent is said carboxylic acid.
 6. The method of claim 1 or 2 wherein the catalyst is an enzyme capable of esterifying the carboxylic acid with the diol to form diol esters of the carboxylic acid.
 7. The method of claim 6 wherein the enzyme is selected from the group consisting of an esterase, a lipase, a phospholipase, and a lysophospholipase.
 8. The method of claim 1 or 2 wherein the hydrolyzing of the diol ester is in the presence of a hydrolysis catalyst.
 9. The method of claim 8 wherein the hydrolysis catalyst is selected from the group consisting of an acid catalyst, an organic acid, a water soluble acid, a water insoluble acid, and base and an enzyme capable of hydrolyzing the diol esters to form a carboxylic acid and a diol.
 10. The method of claim 9 wherein the enzyme is an esterase, lipase, phospholipase, or lysophospholipase.
 11. The method of claim 1 or 2 wherein contacting is in a fermentation product broth wherein the fermentation product broth has been processed to remove the fermentative microorganism, and optionally any additional undissolved solids.
 12. The method of claim 1 or 2 wherein contacting is in a fermentation product broth wherein the fermentation product broth has been processed to reduce protease activity in the broth.
 13. The method of claim 1 or 2 wherein the diol is selected from the group consisting of 1,2-ethanediol, 1,2-propanediol, 1,3-propanediol, 1,4-butanediol, and 2,3-butanediol.
 14. The method of claim 2 wherein solids are separated from the feedstock slurry prior to step (c).
 15. The method of claim 1 or 2 wherein the carboxylic acid is obtained by hydrolysis of oil to carboxylic acid, wherein the oil is an oil stream separated from feedstock slurry or is a native oil.
 16. The method of claim 15 wherein conversion to a carboxylic acid is by a catalyst that is an enzyme capable of esterifying the carboxylic acid with a diol to form diol esters of the carboxylic acid.
 17. The method of claim 16 wherein the enzyme is an esterase, lipase, phospholipase, or lysophospholipase.
 18. The method of claim 15 wherein at least a portion of the oil is converted to glycerol which is used in diol production.
 19. The method of claim 1 or 2 wherein the carboxylic acid comprises at least one fatty acid.
 20. The method of claim 19 wherein the fatty acid is corn oil fatty acid, soya oil fatty acid, or a mixture of corn oil fatty acid and soya oil fatty acid.
 21. The method of claim 14 wherein the solids are processed to form to an animal feed product. 